3V76 | pdb_00003v76

The crystal structure of a flavoprotein from Sinorhizobium meliloti

PDB DOI: https://doi.org/10.2210/pdb3V76/pdb

Classification: FLAVOPROTEIN
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-20 Released: 2012-01-04
Deposition Author(s): Zhang, Z., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.197 (Depositor), 0.196 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of a flavoprotein from Sinorhizobium meliloti

Zhang, Z., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 46.28 kDa
Atom Count: 3,091
Modeled Residue Count: 390
Deposited Residue Count: 417
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavoprotein	A	417	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: R00707, SMc00763
UniProt
Find proteins for Q92RY0 (Rhizobium meliloti (strain 1021)) Explore Q92RY0 Go to UniProtKB: Q92RY0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92RY0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA Query on FDA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.197 (Depositor), 0.196 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.091	α = 90
b = 101.091	β = 90
c = 106.934	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-01-04

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-01-04
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-16
Changes: Structure summary