3RXY | pdb_00003rxy

Crystal structure of NIF3 superfamily protein from Sphaerobacter thermophilus

PDB DOI: https://doi.org/10.2210/pdb3RXY/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Sphaerobacter thermophilus DSM 20745
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-05-10 Released: 2011-06-22
Deposition Author(s): Michalska, K., Tesar, C., Clancy, S., Otwinowski, Z., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.232 (Depositor), 0.241 (DCC)
R-Value Work:
0.209 (Depositor), 0.211 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of NIF3 superfamily protein from Sphaerobacter thermophilus

Michalska, K., Tesar, C., Clancy, S., Otwinowski, Z., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 182.39 kDa
Atom Count: 13,169
Modeled Residue Count: 1,652
Deposited Residue Count: 1,668
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NIF3 protein	A, B, C, D, E A, B, C, D, E, F	278	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0 Gene Names: Sthe_0840
UniProt
Find proteins for D1C210 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C210 Go to UniProtKB: D1C210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1C210
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain AA [auth F]	AA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Interactions & Density Focus chain AA [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain X [auth E] SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain BA [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth E] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth E] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth F]	BA [auth F] G [auth A] I [auth A] J [auth A] K [auth B] BA [auth F], G [auth A], I [auth A], J [auth A], K [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], S [auth D], U [auth D], V [auth E], X [auth E], Y [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain X [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth F] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain X [auth E] Focus chain Y [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain Z [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Z [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A] L [auth B] O [auth B] R [auth C] T [auth D] H [auth A], L [auth B], O [auth B], R [auth C], T [auth D], W [auth E], Z [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	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: 0.232 (Depositor), 0.241 (DCC)
R-Value Work: 0.209 (Depositor), 0.211 (DCC)
R-Value Observed: 0.209 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.77	α = 90
b = 96.483	β = 115.28
c = 128.47	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary