2G7Z | pdb_00002g7z

Conserved DegV-like Protein of Unknown Function from Streptococcus pyogenes M1 GAS Binds Long-chain Fatty Acids

PDB DOI: https://doi.org/10.2210/pdb2G7Z/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Streptococcus pyogenes M1 GAS
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-03-01 Released: 2006-04-04
Deposition Author(s): Nocek, B., Volkart, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.207 (Depositor), 0.211 (DCC)
R-Value Work:
0.165 (Depositor), 0.167 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Conserved hypothetical protein from Streptococcus pyogenes M1 GAS discloses long-fatty acid (heptadecanoic acid) binding function

Nocek, B., Volkart, L., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 63.43 kDa
Atom Count: 4,714
Modeled Residue Count: 550
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein SPy1493	A, B	282	Streptococcus pyogenes M1 GAS	Mutation(s): 7
UniProt
Find proteins for P67372 (Streptococcus pyogenes serotype M1) Explore P67372 Go to UniProtKB: P67372
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P67372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HXA Query on HXA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain W [auth B] MOL2 format, chain O [auth A] MOL2 format, chain W [auth B] mmCIF format, chain O [auth A] mmCIF format, chain W [auth B]	O [auth A], W [auth B]	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID C₂₂ H₃₂ O₂ MBMBGCFOFBJSGT-KUBAVDMBSA-N		Interactions Focus chain O [auth A] Focus chain W [auth B] Interactions & Density Focus chain O [auth A] Focus chain W [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain P [auth A] MOL2 format, chain X [auth B] MOL2 format, chain P [auth A] mmCIF format, chain X [auth B] mmCIF format, chain P [auth A]	P [auth A], X [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain P [auth A] Focus chain X [auth B] Interactions & Density Focus chain P [auth A] Focus chain X [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain Z [auth B] SDF format, chain Y [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B]	Q [auth A], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain Q [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain M [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain M [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain M [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.207 (Depositor), 0.211 (DCC)
R-Value Work: 0.165 (Depositor), 0.167 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.126	α = 90
b = 74.093	β = 90
c = 128.597	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-04-04
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary