5IBZ | pdb_00005ibz

Crystal structure of a novel cyclase (pfam04199).

PDB DOI: https://doi.org/10.2210/pdb5IBZ/pdb

Classification: LYASE
Organism(s): uncultured organism
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-22 Released: 2017-08-09
Deposition Author(s): Nocek, B., Skarina, T., Brown, G., Joachimiak, A., Savchenko, A., Yakunin, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.161 (Depositor), 0.164 (DCC)
R-Value Work:
0.133 (Depositor), 0.137 (DCC)
R-Value Observed:
0.134 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5IBZ

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

Literature

Crystal structure of a novel cyclase (pfam04199).

Nocek, B., Skarina, T., Brown, G., Joachimiak, A., Savchenko, A., Yakunin, A.

To be published.

Macromolecule Content

Total Structure Weight: 141.4 kDa
Atom Count: 11,077
Modeled Residue Count: 1,215
Deposited Residue Count: 1,292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	323	uncultured organism	Mutation(s): 0
UniProt
Find proteins for A0A0G3FEK2 (uncultured organism) Explore A0A0G3FEK2 Go to UniProtKB: A0A0G3FEK2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0G3FEK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
UVW Query on UVW Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], I [auth D]	ACETYLPHOSPHATE C₂ H₅ O₅ P LIPOUNRJVLNBCD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain I [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: 1.61 Å
R-Value Free: 0.161 (Depositor), 0.164 (DCC)
R-Value Work: 0.133 (Depositor), 0.137 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.508	α = 90
b = 120.618	β = 90
c = 148.822	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-08-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-08-09
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

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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.