3IMK | pdb_00003imk

Crystal structure of Putative molybdenum carrier protein (YP_461806.1) from SYNTROPHUS ACIDITROPHICUS SB at 1.45 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3IMK/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Syntrophus aciditrophicus SB
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-10 Released: 2009-08-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal structure of Putative molybdenum carrier protein (YP_461806.1) from SYNTROPHUS ACIDITROPHICUS SB at 1.45 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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.3 kDa 
• Atom Count: 1,536 
• Modeled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative molybdenum carrier protein	A	158	Syntrophus aciditrophicus SB	Mutation(s): 0  Gene Names: SYNAS_17590, SYN_02013, YP_461806.1
UniProt
Find proteins for Q2LU76 (Syntrophus aciditrophicus (strain SB)) Explore Q2LU76  Go to UniProtKB:  Q2LU76

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG6	F [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	B [auth A], C [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: 1.45 Å
• R-Value Free:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33IMK

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.25	α = 90
b = 59.255	β = 90
c = 64.953	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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: 2024-11-20
  Changes: Data collection, Structure summary