1I9C

GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENOSYLCOBALAMIN AND SUBSTRATE

PDB DOI: https://doi.org/10.2210/pdb1I9C/pdb

Classification: ISOMERASE
Organism(s): Clostridium cochlearium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2001-03-19 Released: 2002-03-19
Deposition Author(s): Gruber, K., Kratky, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.221 (Depositor), 0.200 (DCC)
R-Value Work:
0.168 (Depositor), 0.160 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Radical Shuttling in a Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer in the Coenzyme B(12) Dependent Enzyme Glutamate Mutase

Gruber, K., Reitzer, R., Kratky, C.

(2001) Angew Chem Int Ed Engl 40: 3377-3380

PubMed: 11592143 Search on PubMed
DOI: https://doi.org/10.1002/1521-3773(20010917)40:18<3377::aid-anie3377>3.0.co;2-8
Primary Citation of Related Structures:
1I9C

Organizational Affiliation

Institut für Chemie Universität Graz Heinrichstrasse 28, 8010 Graz (Austria).

Macromolecule Content

Total Structure Weight: 140.66 kDa
Atom Count: 11,290
Modelled Residue Count: 1,240
Deposited Residue Count: 1,240
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE MUTASE	A, C	137	Clostridium cochlearium	Mutation(s): 0 Gene Names: GLMS EC: 5.4.99.1
UniProt
Find proteins for P80078 (Clostridium cochlearium) Explore P80078 Go to UniProtKB: P80078
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80078
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE MUTASE	B, D	483	Clostridium cochlearium	Mutation(s): 0 Gene Names: GLME EC: 5.4.99.1
UniProt
Find proteins for P80077 (Clostridium cochlearium) Explore P80077 Go to UniProtKB: P80077
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80077
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 Query on B12 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C]	E [auth A], I [auth C]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]
5AD Query on 5AD Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain J [auth D] MOL2 format, chain F [auth B] MOL2 format, chain J [auth D] mmCIF format, chain F [auth B] mmCIF format, chain J [auth D]	F [auth B], J [auth D]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain F [auth B] Focus chain J [auth D] Interactions & Density Focus chain F [auth B] Focus chain J [auth D]
2AS Query on 2AS Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D]	H [auth B], L [auth D]	(2S,3S)-3-methyl-aspartic acid C₅ H₉ N O₄ LXRUAYBIUSUULX-HRFVKAFMSA-N		Interactions Focus chain H [auth B] Focus chain L [auth D] Interactions & Density Focus chain H [auth B] Focus chain L [auth D]
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D]	G [auth B], K [auth D]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.221 (Depositor), 0.200 (DCC)
R-Value Work: 0.168 (Depositor), 0.160 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.348	α = 90
b = 113.139	β = 96
c = 108.439	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-03-19

Deposition Author(s):

Gruber, K.

Kratky, C.

Revision History (Full details and data files)

Version 1.0: 2002-03-19
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2012-10-24
Changes: Non-polymer description
Version 1.4: 2019-07-24
Changes: Data collection, Refinement description
Version 1.5: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description