2HX5 | pdb_00002hx5

Crystal structure of a putative thioesterase (pmt_2055) from prochlorococcus marinus str. mit 9313 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2HX5/pdb

• Classification: HYDROLASE
• Organism(s): Prochlorococcus marinus str. MIT 9313
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-08-02 Released: 2006-08-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.170 (DCC) 

Literature

Crystal structure of hypothetical protein (NP_895880.1) from Prochlorococcus marinus MIT9313 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.71 kDa 
• Atom Count: 1,381 
• Modeled Residue Count: 144 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A	152	Prochlorococcus marinus str. MIT 9313	Mutation(s): 3  Gene Names: NP_895880.1 EC: 3.1.2.28
UniProt
Find proteins for Q7V4A7 (Prochlorococcus marinus (strain MIT 9313)) Explore Q7V4A7  Go to UniProtKB:  Q7V4A7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETX	B [auth A], C [auth A]	2-ETHOXYETHANOL C4 H10 O2 ZNQVEEAIQZEUHB-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.170 (DCC) 

Diffraction Data: https://doi.org/10.18430/M32HX5

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.22	α = 90
b = 104.22	β = 90
c = 104.22	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-08-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-20
  Changes: Data collection, Structure summary