2IGT | pdb_00002igt

Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens

PDB DOI: https://doi.org/10.2210/pdb2IGT/pdb

Classification: TRANSFERASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-09-25 Released: 2006-10-24
Deposition Author(s): Kim, Y., Joachimiak, A., Xu, X., Gu, J., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.192 (Depositor), 0.192 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens

Kim, Y., Joachimiak, A., Xu, X., Gu, J., Edwards, A., Savchenko, A.

To be published.

Macromolecule Content

Total Structure Weight: 114.36 kDa
Atom Count: 9,249
Modeled Residue Count: 938
Deposited Residue Count: 996
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM dependent methyltransferase	A, B, C	332	Agrobacterium fabrum str. C58	Mutation(s): 7
UniProt
Find proteins for A9CKD6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CKD6 Go to UniProtKB: A9CKD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9CKD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 J [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C]	D [auth A], J [auth B], N [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain N [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain E [auth A] MOL2 format, chain O [auth C] MOL2 format, chain E [auth A] mmCIF format, chain O [auth C] mmCIF format, chain E [auth A]	E [auth A], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] P [auth C] Q [auth C] F [auth A], G [auth A], H [auth A], P [auth C], Q [auth C], R [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] L [auth B] M [auth B] S [auth C] I [auth A], K [auth B], L [auth B], M [auth B], S [auth C], T [auth C], U [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.192 (Depositor), 0.192 (DCC)
R-Value Work: 0.162 (Depositor), 0.162 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.941	α = 90
b = 145.555	β = 90
c = 204.895	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
MLPHARE	phasing
Coot	model building
ARP/wARP	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-10-24

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-10-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary