2ZUM

Functional Analysis of Hyperthermophilic Endocellulase from the Archaeon Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb2ZUM/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-10-21 Released: 2009-11-03
Deposition Author(s): Kim, H.-W., Ishikawa, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.221
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of hyperthermophilic endocellulase from Pyrococcus horikoshii

Kim, H.-W., Ishikawa, K.

(2009) Proteins 78: 496-500

PubMed: 19847920 Search on PubMed
DOI: https://doi.org/10.1002/prot.22602
Primary Citation of Related Structures:
2ZUM

Organizational Affiliation

National Institute of Advanced Industrial Science and Technology (AIST), 1-18-31, Midorigaoka, Ikeda, Osaka 563-8577, Japan.

Macromolecule Content

Total Structure Weight: 53.33 kDa
Atom Count: 3,654
Modelled Residue Count: 378
Deposited Residue Count: 458
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
458aa long hypothetical endo-1,4-beta-glucanase	A	458	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: EGPh EC: 3.2.1.4
UniProt
Find proteins for O58925 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58925 Go to UniProtKB: O58925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	K [auth A] L [auth A] M [auth A] O [auth A] P [auth A] K [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain N [auth A] MOL2 format, chain B [auth A] MOL2 format, chain N [auth A] mmCIF format, chain B [auth A] mmCIF format, chain N [auth A]	B [auth A], N [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain N [auth A] Interactions & Density Focus chain B [auth A] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.221
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.15	α = 90
b = 77.15	β = 90
c = 161.105	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-03

Deposition Author(s):

Kim, H.-W.

Ishikawa, K.

Revision History (Full details and data files)

Version 1.0: 2009-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary