1NJK | pdb_00001njk

Crystal Structure of YbaW Probable Thioesterase from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb1NJK/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-12-31 Released: 2003-07-01
Deposition Author(s): Kim, Y., Joachimiak, A., Edwards, A., Xu, X., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.240 (Depositor), 0.236 (DCC)
R-Value Work:
0.214 (Depositor), 0.210 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Escherichia coli Hypothetical Protein YbaW

Kim, Y., Joachimiak, A., Edwards, A., Xu, X., Savchenko, A.

To be published.

Macromolecule Content

Total Structure Weight: 72.54 kDa
Atom Count: 4,643
Modeled Residue Count: 532
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ybaW	A, B, C, D	156	Escherichia coli	Mutation(s): 3 Gene Names: YBAW EC: 3.1.2
UniProt
Find proteins for P77712 (Escherichia coli (strain K12)) Explore P77712 Go to UniProtKB: P77712
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P77712
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth B], F [auth C], G [auth C], H [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth D]

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: 1.90 Å
R-Value Free: 0.240 (Depositor), 0.236 (DCC)
R-Value Work: 0.214 (Depositor), 0.210 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.134	α = 90
b = 90.134	β = 90
c = 83.373	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-07-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2003-07-01
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

1NJK | pdb_00001njk

Crystal Structure of YbaW Probable Thioesterase from Escherichia coli

Literature

Crystal Structure of Escherichia coli Hypothetical Protein YbaW

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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