1ZGH

Methionyl-tRNA formyltransferase from Clostridium thermocellum

PDB DOI: https://doi.org/10.2210/pdb1ZGH/pdb
Entry: 1ZGH supersedes: 1XG9

Classification: TRANSFERASE
Organism(s): Acetivibrio thermocellus ATCC 27405
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2005-04-21 Released: 2005-05-03
Deposition Author(s): Yang, H., Kataeva, I., Xu, H., Zhao, M., Chang, J., Liu, Z., Chen, L., Tempel, W., Habel, J., Zhou, W., Lee, D., Lin, D., Chang, S., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Wang, B., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.237
R-Value Work: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Methionyl-tRNA formyltransferase from Clostridium thermocellum

Yang, H., Kataeva, I., Xu, H., Zhao, M., Chang, J., Liu, Z., Chen, L., Tempel, W., Habel, J., Zhou, W., Lee, D., Lin, D., Chang, S., Arendall III, W.B., Richardson, J.S., Richardson, D.C., Rose, J.P., Wang, B., Southeast Collaboratory for Structural Genomics

To be published.

Macromolecule Content

Total Structure Weight: 30.35 kDa
Atom Count: 1,873
Modelled Residue Count: 227
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA formyltransferase	A	260	Acetivibrio thermocellus ATCC 27405	Mutation(s): 6
UniProt
Find proteins for A3DHJ7 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DHJ7 Go to UniProtKB: A3DHJ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3DHJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.237
R-Value Work: 0.209
Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.396	α = 90
b = 85.396	β = 90
c = 104.27	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-05-03

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

This entry supersedes: 1XG9

Revision History (Full details and data files)

Version 1.0: 2005-05-03
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description