3AKP

Crystal structure of xylanase from Trichoderma longibrachiatum

PDB DOI: https://doi.org/10.2210/pdb3AKP/pdb

Classification: HYDROLASE
Organism(s): Trichoderma longibrachiatum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-15 Released: 2011-06-01
Deposition Author(s): Sugahara, M., Kunishima, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.196
R-Value Work: 0.181
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Packing Space Expansion of Protein Crystallization Screening with Synthetic Zeolite as a Heteroepitaxic Nucleant

Sugahara, M., Kageyama-Morikawa, Y., Kunishima, N.

(2011) Cryst Growth Des 11: 110-120

DOI: https://doi.org/10.1021/cg100987g

Macromolecule Content

Total Structure Weight: 41.95 kDa
Atom Count: 3,504
Modelled Residue Count: 380
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
xylanase	A, B	190	Trichoderma longibrachiatum	Mutation(s): 0 EC: 3.2.1.8
UniProt
Find proteins for F8W669 (Trichoderma longibrachiatum) Explore F8W669 Go to UniProtKB: F8W669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8W669
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A, B	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.196
R-Value Work: 0.181
R-Value Observed: 0.181
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.657	α = 90
b = 38.831	β = 94.78
c = 81.254	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.