3I4K | pdb_00003i4k

Crystal structure of Muconate lactonizing enzyme from Corynebacterium glutamicum

PDB DOI: https://doi.org/10.2210/pdb3I4K/pdb

Classification: ISOMERASE
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-01 Released: 2009-07-14
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.277 (Depositor), 0.276 (DCC)
R-Value Work:
0.244 (Depositor), 0.244 (DCC)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Muconate lactonizing enzyme from Corynebacterium glutamicum

Fedorov, A.A., Fedorov, E.V., Sauder, J.M., Burley, S.K., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 335.22 kDa
Atom Count: 23,024
Modeled Residue Count: 2,960
Deposited Residue Count: 3,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muconate lactonizing enzyme	A, B, C, D, E A, B, C, D, E, F, G, H	383	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: catB, Cgl2401, cg2635 EC: 5.5.1.1 (PDB Primary Data), 5.5.1.7 (PDB Primary Data)
UniProt
Find proteins for Q8NN12 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NN12 Go to UniProtKB: Q8NN12
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NN12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.277 (Depositor), 0.276 (DCC)
R-Value Work: 0.244 (Depositor), 0.244 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.541	α = 90
b = 156.709	β = 90
c = 202.952	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Structure summary