2X7M | pdb_00002x7m

Crystal structure of Archaemetzincin (amzA) from Methanopyrus kandleri at 1.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb2X7M/pdb

Classification: HYDROLASE
Organism(s): Methanopyrus kandleri AV19
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-03-01 Released: 2010-06-09
Deposition Author(s): Waltersperger, S.M., Widmer, C., Baumann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.203 (Depositor)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2X7M

This is version 2.0 of the entry. See complete history.

Literature

Crystal Structure of Archaemetzincin Amza from Methanopyrus Kandleri at 1.5A Resolution.

Waltersperger, S.M., Widmer, C., Baumann, U.

(2010) Proteins 78: 2720

PubMed: 20597090 Search on PubMed
DOI: https://doi.org/10.1002/prot.22777
Primary Citation Related Structures:
2X7M

Organizational Affiliation

Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland.

Macromolecule Content

Total Structure Weight: 22.16 kDa
Atom Count: 1,534
Modeled Residue Count: 180
Deposited Residue Count: 195
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARCHAEMETZINCIN	A	195	Methanopyrus kandleri AV19	Mutation(s): 0 EC: 3 (PDB Primary Data), 3.4 (UniProt)
UniProt
Find proteins for Q8TXW1 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore Q8TXW1 Go to UniProtKB: Q8TXW1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TXW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.203 (Depositor)
R-Value Work: 0.176 (Depositor)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.51	α = 90
b = 55.08	β = 90
c = 58.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing
SHELXE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-06-09

Deposition Author(s):

Waltersperger, S.M.

Revision History (Full details and data files)

Version 1.0: 2010-06-09
Type: Initial release
Version 1.1: 2011-09-28
Changes: Database references, Refinement description, Version format compliance
Version 2.0: 2024-05-08
Changes: Atomic model, Data collection, Database references, Derived calculations, Other

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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.