3SIY

Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3SIY/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Ruegeria sp. TM1040
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-20 Released: 2011-07-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.172 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 

Literature

Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 105.78 kDa 
• Atom Count: 8,384 
• Modelled Residue Count: 923 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF1989 family protein	A, B, C, D	234	Ruegeria sp. TM1040	Mutation(s): 0  Gene Names: TM1040_0329
UniProt
Find proteins for Q1GJV4 (Ruegeria sp. (strain TM1040)) Explore Q1GJV4  Go to UniProtKB:  Q1GJV4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], G [auth B], J [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], H [auth B], I [auth B], L [auth C], M [auth C], O [auth D], P [auth D], Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.172 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M33SIY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.907	α = 90
b = 48.132	β = 98.44
c = 144.732	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
MolProbity	model building
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations