4O29 | pdb_00004o29

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE from Pyrobaculum aerophilum in COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE

PDB DOI: https://doi.org/10.2210/pdb4O29/pdb

Classification: TRANSFERASE
Organism(s): Pyrobaculum aerophilum str. IM2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-17 Released: 2014-01-15
Deposition Author(s): Sawaya, M.R., Yeates, T.O., Griffith, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.261 (Depositor), 0.280 (DCC)
R-Value Work:
0.210 (Depositor), 0.226 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of L-isoaspartyl (D-aspartyl) Methyltransferase

(2002) Thesis University of California, Los Angeles: 93-107

Macromolecule Content

Total Structure Weight: 23.62 kDa
Atom Count: 1,635
Modeled Residue Count: 207
Deposited Residue Count: 208
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-L-isoaspartate O-methyltransferase	A	208	Pyrobaculum aerophilum str. IM2	Mutation(s): 0 Gene Names: PAE0701, pcm, PIMT EC: 2.1.1.77
UniProt
Find proteins for Q8ZYN0 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZYN0 Go to UniProtKB: Q8ZYN0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZYN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.261 (Depositor), 0.280 (DCC)
R-Value Work: 0.210 (Depositor), 0.226 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.72	α = 90
b = 35.67	β = 100.31
c = 66.29	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
EPMR	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2017-10-11
Changes: Data collection
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.