3SIY | pdb_00003siy

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.172 (Depositor), 0.170 (DCC)
R-Value Work:
0.137 (Depositor), 0.140 (DCC)
R-Value Observed:
0.139 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain N [auth D]	E [auth A], G [auth B], J [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth A] H [auth B] I [auth B] L [auth C] M [auth C] 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		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.170 (DCC)
R-Value Work: 0.137 (Depositor), 0.140 (DCC)
R-Value Observed: 0.139 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33SIY

Space Group: C 1 2 1

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-07-13

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary