2OC5 | pdb_00002oc5

Crystal structure of a ferritin-like protein (pmt1231) from prochlorococcus marinus str. mit 9313 at 1.68 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OC5/pdb

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


• Deposited: 2006-12-20 Released: 2007-02-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.200 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Crystal structure of hypothetical protein (NP_895059.1) from Prochlorococcus marinus MIT9313 at 1.68 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.81 kDa 
• Atom Count: 2,158 
• Modeled Residue Count: 222 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A	244	Prochlorococcus marinus str. MIT 9313	Mutation(s): 8  Gene Names: NP_895059.1 EC: 4.1.99.5
UniProt
Find proteins for Q7V6D4 (Prochlorococcus marinus (strain MIT 9313)) Explore Q7V6D4  Go to UniProtKB:  Q7V6D4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
UNL	E [auth A]	Unknown ligand VTLYFUHAOXGGBS-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: 1.68 Å
• R-Value Free:  0.200 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32OC5

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.35	α = 90
b = 77.35	β = 90
c = 116.89	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-02-13
  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: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary