4NT9 | pdb_00004nt9

Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia

PDB DOI: https://doi.org/10.2210/pdb4NT9/pdb

Classification: HYDROLASE
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-02 Released: 2014-11-12
Deposition Author(s): Yang, Y.H., Zhang, J., Jiang, Y.L., Zhou, C.Z., Chen, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.212 (Depositor), 0.211 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4NT9

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia

Yang, Y.H., Zhang, J., Jiang, Y.L., Zhou, C.Z., Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 74.13 kDa
Atom Count: 4,833
Modeled Residue Count: 552
Deposited Residue Count: 657
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A [auth B], B [auth A], C	219	Streptococcus pneumoniae TIGR4	Mutation(s): 0 Gene Names: SP_0629
UniProt
Find proteins for A0A0H2UP74 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UP74 Go to UniProtKB: A0A0H2UP74
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UP74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain F [auth B] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain F [auth B] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain F [auth B]	F [auth B], I [auth A], J [auth A], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Interactions & Density Focus chain F [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain G [auth A] SDF format, chain D [auth B] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain D [auth B] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain D [auth B]	D [auth B], G [auth A], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain G [auth A] Focus chain K [auth C] Interactions & Density Focus chain D [auth B] Focus chain G [auth A] Focus chain K [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain H [auth A] SDF format, chain E [auth B] MOL2 format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain E [auth B] mmCIF format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain E [auth B]	E [auth B], H [auth A], L [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain H [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth B] Focus chain H [auth A] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.212 (Depositor), 0.211 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.11	α = 90
b = 68.08	β = 108.41
c = 80.35	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.