1SG9

Crystal structure of Thermotoga maritima protein HEMK, an N5-glutamine methyltransferase

PDB DOI: https://doi.org/10.2210/pdb1SG9/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-02-23 Released: 2004-08-17
Deposition Author(s): Agarwal, R., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.261
R-Value Work: 0.235
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.

Agarwal, R., Burley, S.K., Swaminathan, S.

(2008) Proteins 71: 1038-1041

PubMed: 18247349 Search on PubMed
DOI: https://doi.org/10.1002/prot.21962
Primary Citation of Related Structures:
1SG9

Organizational Affiliation

Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Macromolecule Content

Total Structure Weight: 96.59 kDa
Atom Count: 6,841
Modelled Residue Count: 822
Deposited Residue Count: 846
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemK protein	A, B, C	282	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9WYV8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYV8 Go to UniProtKB: Q9WYV8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYV8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C]	D [auth A], F [auth B], H [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C]
GLN Query on GLN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C]	E [auth A], G [auth B], I [auth C]	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.261
R-Value Work: 0.235
R-Value Observed: 0.235
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.025	α = 90
b = 188.332	β = 90
c = 207.684	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MARMAD	data reduction
ADSC	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-08-17

Deposition Author(s):

Agarwal, R.

Swaminathan, S.

Burley, S.K.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-08-17
Type: Initial release
Version 1.1: 2008-07-14
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references

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1SG9

Crystal structure of Thermotoga maritima protein HEMK, an N5-glutamine methyltransferase

A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)