3HDP | pdb_00003hdp

Crystal structure of the NI(II)-bound Glyoxalase-I from Clostridium acetobutylicum

PDB DOI: https://doi.org/10.2210/pdb3HDP/pdb

Classification: LYASE
Organism(s): Clostridium acetobutylicum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-05-07 Released: 2009-05-26
Deposition Author(s): Satyanarayana, L., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.286 (Depositor), 0.269 (DCC)
R-Value Work:
0.252 (Depositor), 0.236 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the NI(II)-bound Glyoxalase-I from Clostridium acetobutylicum.

Satyanarayana, L., Eswaramoorthy, S., Honek, J., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 15.17 kDa
Atom Count: 1,139
Modeled Residue Count: 132
Deposited Residue Count: 133
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase-I	A	133	Clostridium acetobutylicum	Mutation(s): 0 Gene Names: CAC2192, CA_C2192 EC: 4.4.1.5
UniProt
Find proteins for Q97H22 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97H22 Go to UniProtKB: Q97H22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97H22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.286 (Depositor), 0.269 (DCC)
R-Value Work: 0.252 (Depositor), 0.236 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.269	α = 90
b = 70.269	β = 90
c = 66.589	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Satyanarayana, L.

Eswaramoorthy, S.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description

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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.