3GIU | pdb_00003giu

1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3GIU/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-06 Released: 2009-03-17
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.148 (Depositor), 0.177 (DCC)
R-Value Work:
0.116 (Depositor), 0.150 (DCC)
R-Value Observed:
0.118 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

1.25 Angstrom Crystal Structure of Pyrrolidone-Carboxylate Peptidase (pcp) from Staphylococcus aureus

Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 48.33 kDa
Atom Count: 4,362
Modeled Residue Count: 425
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrrolidone-carboxylate peptidase	A, B	215	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: pcp, SACOL2714 EC: 3.4.19.3
UniProt
Find proteins for Q5HCK7 (Staphylococcus aureus (strain COL)) Explore Q5HCK7 Go to UniProtKB: Q5HCK7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HCK7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], K [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.148 (Depositor), 0.177 (DCC)
R-Value Work: 0.116 (Depositor), 0.150 (DCC)
R-Value Observed: 0.118 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.79	α = 90
b = 81	β = 90
c = 119.91	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SHARP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-17

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-03-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Advisory, Refinement description
Version 1.3: 2024-11-06
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary