3E49 | pdb_00003e49

Crystal structure of a prokaryotic domain of unknown function (duf849) with a tim barrel fold (bxe_c0966) from burkholderia xenovorans lb400 at 1.75 A resolution

PDB DOI: https://doi.org/10.2210/pdb3E49/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-11 Released: 2008-08-26
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_556190.1) from BURKHOLDERIA XENOVORANS LB400 at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 138.99 kDa
Atom Count: 10,552
Modeled Residue Count: 1,228
Deposited Residue Count: 1,244
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein DUF849 with a TIM barrel fold	A, B, C, D	311	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: YP_556190.1, Bxeno_C0912, Bxe_C0966
UniProt
Find proteins for Q13GE9 (Paraburkholderia xenovorans (strain LB400)) Explore Q13GE9 Go to UniProtKB: Q13GE9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13GE9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ETX Query on ETX Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain H [auth B]	F [auth A] H [auth B] I [auth B] J [auth B] N [auth C] F [auth A], H [auth B], I [auth B], J [auth B], N [auth C], O [auth C], P [auth C]	2-ETHOXYETHANOL C₄ H₁₀ O₂ ZNQVEEAIQZEUHB-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B]	L [auth B], R [auth C], T [auth D], U [auth D], V [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain L [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain L [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] SDF format, chain S [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain S [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain S [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], M [auth C], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain M [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain M [auth C] Focus chain S [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C]	K [auth B], Q [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain Q [auth C] Interactions & Density Focus chain K [auth B] Focus chain Q [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33E49

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.495	α = 69.99
b = 68.275	β = 88.07
c = 83.952	γ = 72.84

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary