2UZ0 | pdb_00002uz0

The Crystal crystal structure of the estA protein, a virulence factor estA protein from Streptococcus pneumonia

PDB DOI: https://doi.org/10.2210/pdb2UZ0/pdb

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

Deposited: 2007-04-23 Released: 2007-10-23
Deposition Author(s): Kim, M.H., Kang, B.S., Kim, K.J., Oh, T.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.213 (Depositor), 0.208 (DCC)
R-Value Work:
0.183 (Depositor), 0.179 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structure of the Esta Protein, a Virulence Factor from Streptococcus Pneumoniae.

Kim, M.H., Kang, B.S., Kim, S., Kim, K.J., Lee, C.H., Oh, B.C., Park, S.C., Oh, T.K.

(2008) Proteins 70: 578

PubMed: 17932928 Search on PubMed
DOI: https://doi.org/10.1002/prot.21680
Primary Citation Related Structures:
2UZ0

Organizational Affiliation

Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.

Macromolecule Content

Total Structure Weight: 123.28 kDa
Atom Count: 8,765
Modeled Residue Count: 999
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIBUTYRIN ESTERASE	A, B, C, D	263	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for A0A0H2UNZ8 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UNZ8 Go to UniProtKB: A0A0H2UNZ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UNZ8
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 P [auth D] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] K [auth C] L [auth C] O [auth D] F [auth A], G [auth A], K [auth C], L [auth C], O [auth D], P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B], M [auth C], N [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213 (Depositor), 0.208 (DCC)
R-Value Work: 0.183 (Depositor), 0.179 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.695	α = 90
b = 72.128	β = 94.31
c = 101.827	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Other, Structure summary

2UZ0 | pdb_00002uz0

The Crystal crystal structure of the estA protein, a virulence factor estA protein from Streptococcus pneumonia

Literature

The Crystal Structure of the Esta Protein, a Virulence Factor from Streptococcus Pneumoniae.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand