1WCZ | pdb_00001wcz

Crystal structure of an alkaline form of v8 protease from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb1WCZ/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Mutation(s): No

Deposited: 2004-05-10 Released: 2004-06-01
Deposition Author(s): Yamada, K., Ohta, M., Hasegawa, T., Torii, K., Murakami, M., Kouyama, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.212 (Depositor)

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

Literature

Crystal structure of an alkaline form of v8 protease from Staphylococcus aureus

Yamada, K., Ohta, M., Hasegawa, T., Torii, K., Murakami, M., Kouyama, K.

To be published.

Macromolecule Content

Total Structure Weight: 29.09 kDa
Atom Count: 1,817
Modeled Residue Count: 215
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl endopeptidase	A	268	Staphylococcus aureus	Mutation(s): 0 EC: 3.4.21.19
UniProt
Find proteins for P0C1U8 (Staphylococcus aureus) Explore P0C1U8 Go to UniProtKB: P0C1U8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C1U8
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.00 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.29	α = 90
b = 61.29	β = 90
c = 221.13	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-06-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-06-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, 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.