3VIS | pdb_00003vis

Crystal structure of cutinase Est119 from Thermobifida alba AHK119

PDB DOI: https://doi.org/10.2210/pdb3VIS/pdb

Classification: HYDROLASE
Organism(s): Thermobifida alba
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-11 Released: 2012-04-11
Deposition Author(s): Kitadokoro, K., Thumarat, U., Nakamura, R., Nishimura, K., Karatani, H., Suzuki, H., Kawai, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.196 (Depositor), 0.195 (DCC)
R-Value Work:
0.150 (Depositor), 0.150 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3VIS

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

Literature

Crystal structure of cutinase Est119 from Thermobida alba AHK119 that can degrade modpolyethylene terephthalate at 1.76 A resolution.

Kitadokoro, K., Thumarat, U., Nakamura, R., Nishimura, K., Karatani, H., Suzuki, H., Kawai, F.

(2012) Polym Degrad Stab 97: 771-775

DOI: https://doi.org/10.1016/j.polymdegradstab.2012.02.003

Macromolecule Content

Total Structure Weight: 66.78 kDa
Atom Count: 4,498
Modeled Residue Count: 522
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase	A, B	306	Thermobifida alba	Mutation(s): 0 Gene Names: est2 EC: 3.1.1.101 (UniProt), 3.1.1.74 (UniProt)
UniProt
Find proteins for F7IX06 (Thermobifida alba) Explore F7IX06 Go to UniProtKB: F7IX06
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F7IX06
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 Query on PE4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.196 (Depositor), 0.195 (DCC)
R-Value Work: 0.150 (Depositor), 0.150 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.989	α = 90
b = 88.732	β = 133.03
c = 71.794	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-04-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-04-11
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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.