3TOQ | pdb_00003toq

Acylphosphatase with mesophilic surface and thermophilic core

PDB DOI: https://doi.org/10.2210/pdb3TOQ/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-09-06 Released: 2012-09-05
Deposition Author(s): Yu, T.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.209 (Depositor), 0.200 (DCC)
R-Value Work:
0.167 (Depositor), 0.160 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Protein surface is the preferred region for thermostability engineering

Yu, T.H., Wong, K.B.

To be published.

Macromolecule Content

Total Structure Weight: 11.28 kDa
Atom Count: 887
Modeled Residue Count: 95
Deposited Residue Count: 99
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylphosphatase-1	A	99	Homo sapiens	Mutation(s): 8 Gene Names: ACYP1, ACYPE EC: 3.6.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P07311 (Homo sapiens) Explore P07311 Go to UniProtKB: P07311
PHAROS: P07311 GTEx: ENSG00000119640
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07311
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.209 (Depositor), 0.200 (DCC)
R-Value Work: 0.167 (Depositor), 0.160 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.1	α = 90
b = 78.1	β = 90
c = 65.577	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.