2NVN | pdb_00002nvn

Crystal structure of a protein with a cupin-like fold and unknown function (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2NVN/pdb

• Classification: Structural Genomics/Unknown function
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-13 Released: 2006-12-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal structure of hypothetical protein (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.62 kDa 
• Atom Count: 987 
• Modeled Residue Count: 121 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A	122	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 3  Gene Names: YP_400729.1
UniProt
Find proteins for Q31MH7 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31MH7  Go to UniProtKB:  Q31MH7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.50 Å
• R-Value Free:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32NVN

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.18	α = 90
b = 82.18	β = 90
c = 80.5	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: 2006-12-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-12-12
  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: 2024-11-13
  Changes: Data collection, Structure summary