2P7H

Crystal structure of a sam dependent methyl-transferase type 12 family protein (eca1738) from pectobacterium atrosepticum scri1043 at 1.85 A resolution

PDB DOI: https://doi.org/10.2210/pdb2P7H/pdb

Classification: TRANSFERASE
Organism(s): Pectobacterium atrosepticum SCRI1043
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-20 Released: 2007-04-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.183
R-Value Work: 0.149
R-Value Observed: 0.150

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of hypothetical protein (YP_049838.1) from Erwinia carotovora atroseptica SCRI1043 at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 115.89 kDa
Atom Count: 8,165
Modelled Residue Count: 910
Deposited Residue Count: 1,000
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C, D	250	Pectobacterium atrosepticum SCRI1043	Mutation(s): 4 Gene Names: YP_049838.1, ECA1738
UniProt
Find proteins for Q6D6E7 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D6E7 Go to UniProtKB: Q6D6E7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6D6E7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	F [auth A], K [auth B], O [auth C], S [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	G [auth A] L [auth B] M [auth B] P [auth C] T [auth D] G [auth A], L [auth B], M [auth B], P [auth C], T [auth D], U [auth D], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	E [auth A], H [auth B], I [auth B], N [auth C], Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth C] Focus chain Q [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain R [auth D] MOL2 format, chain J [auth B] MOL2 format, chain R [auth D] mmCIF format, chain J [auth B] mmCIF format, chain R [auth D]	J [auth B], R [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain R [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.183
R-Value Work: 0.149
R-Value Observed: 0.150
Space Group: P 4 2₁ 2
Diffraction Data: https://doi.org/10.18430/M32P7H

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.949	α = 90
b = 117.949	β = 90
c = 150.532	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-04-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary