1RVK | pdb_00001rvk

Crystal structure of enolase AGR_L_2751 from Agrobacterium Tumefaciens

PDB DOI: https://doi.org/10.2210/pdb1RVK/pdb

Classification: structural genomics, unknown function
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-12-14 Released: 2003-12-23
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Thirumuruhan, R., Zencheck, W., Millikin, C., Gerlt, J.A., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.212 (Depositor)
R-Value Work:
0.193 (Depositor)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1RVK

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

Literature

Evolution of enzymatic activites in the Enolase superfamily: 1.7 A crystal structure of the hypothetical protein MR.GI-17937161 from Agrobacterium tumefaciens

Fedorov, A.A., Fedorov, E.V., Thirumuruhan, R., Zencheck, W., Millikin, C., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 43.5 kDa
Atom Count: 3,393
Modeled Residue Count: 381
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isomerase/lactonizing enzyme	A	382	Agrobacterium fabrum str. C58	Mutation(s): 11
UniProt
Find proteins for Q7CSI0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CSI0 Go to UniProtKB: Q7CSI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7CSI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions 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: 1.70 Å
R-Value Free: 0.212 (Depositor)
R-Value Work: 0.193 (Depositor)
R-Value Observed: 0.195 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.733	α = 90
b = 118.733	β = 90
c = 133.199	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-12-23

Deposition Author(s):

Thirumuruhan, R.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2003-12-23
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.