3F7C | pdb_00003f7c

Crystal structure of a duf416 family protein (maqu_0942) from marinobacter aquaeolei vt8 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3F7C/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Marinobacter nauticus VT8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-07 Released: 2008-11-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Crystal structure of protein of unknown function (DUF416) (YP_958225.1) from MARINOBACTER AQUAEOLEI VT8 at 2.00 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.99 kDa 
• Atom Count: 1,714 
• Modeled Residue Count: 199 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein of unknown function (DUF416)	A	200	Marinobacter nauticus VT8	Mutation(s): 0  Gene Names: Maqu_0942, YP_958225.1
UniProt
Find proteins for A1TZ69 (Marinobacter nauticus (strain ATCC 700491 / DSM 11845 / VT8)) Explore A1TZ69  Go to UniProtKB:  A1TZ69

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.00 Å
• R-Value Free:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33F7C

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.998	α = 90
b = 76.998	β = 90
c = 91.26	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, 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: 2024-11-13
  Changes: Data collection, Structure summary