2ZAD | pdb_00002zad

Crystal Structure of Muconate Cycloisomerase from Thermotoga maritima MSB8

PDB DOI: https://doi.org/10.2210/pdb2ZAD/pdb

Classification: ISOMERASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-10-03 Released: 2008-04-08
Deposition Author(s): Padmanabhan, B., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.201 (Depositor), 0.206 (DCC)
R-Value Work:
0.175 (Depositor), 0.181 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Muconate Cycloisomerase from Thermotoga maritima MSB8

Padmanabhan, B., Bessho, Y., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 159.82 kDa
Atom Count: 12,336
Modeled Residue Count: 1,376
Deposited Residue Count: 1,380
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muconate cycloisomerase	A, B, C, D	345	Thermotoga maritima MSB8	Mutation(s): 0 EC: 5.5.1.1 (PDB Primary Data), 5.1.1.20 (UniProt)
UniProt
Find proteins for Q9WXM1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXM1 Go to UniProtKB: Q9WXM1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WXM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], R [auth C], T [auth D], U [auth D], V [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain W [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain W [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain W [auth D]	I [auth A], J [auth A], N [auth B], W [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain W [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	E [auth A], K [auth B], O [auth C], S [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [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: 1.60 Å
R-Value Free: 0.201 (Depositor), 0.206 (DCC)
R-Value Work: 0.175 (Depositor), 0.181 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.77	α = 90
b = 112.77	β = 90
c = 122.526	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-04-08

Deposition Author(s):

Padmanabhan, B.

Bessho, Y.

Yokoyama, S.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-04-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary