6VE6 | pdb_00006ve6

A structural characterization of poly(aspartic acid) hydrolase-1 from Sphingomonas sp. KT-1.

PDB DOI: https://doi.org/10.2210/pdb6VE6/pdb

Classification: HYDROLASE
Organism(s): Sphingomonas sp. KT-1
Expression System: Sphingomonas sp. KT-1
Mutation(s): No

Deposited: 2019-12-28 Released: 2020-12-09
Deposition Author(s): Bolay, A.L., Salvo, H., Brambley, C.A., Yared, T.J., Miller, J.M., Wallen, J.R., Weiland, M.H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.290 (Depositor), 0.291 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6VE6

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

Literature

Structural Characterization of Sphingomonas sp. KT-1 PahZ1-Catalyzed Biodegradation of Thermally Synthesized Poly(aspartic acid)

Brambley, C.A., Bolay, A.L., Salvo, H., Jansch, A.L., Yared, T.J., Miller, J.M., Wallen, J.R., Weiland, M.H.

(2020) ACS Sustain Chem Eng

DOI: https://doi.org/10.1021/acssuschemeng.0c01158

Macromolecule Content

Total Structure Weight: 131.1 kDa
Atom Count: 8,833
Modeled Residue Count: 1,062
Deposited Residue Count: 1,180
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(Aspartic acid) hydrolase-1	A, B, C, D	295	Sphingomonas sp. KT-1	Mutation(s): 0 Gene Names: pahZ
UniProt
Find proteins for Q7WSC1 (Sphingomonas sp. KT-1) Explore Q7WSC1 Go to UniProtKB: Q7WSC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7WSC1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.290 (Depositor), 0.291 (DCC)
R-Value Work: 0.236 (Depositor), 0.236 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.749	α = 90
b = 87.006	β = 90
c = 171.06	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DUE 1611988

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.