5JX5 | pdb_00005jx5

GH6 Orpinomyces sp. Y102 enzyme

PDB DOI: https://doi.org/10.2210/pdb5JX5/pdb

Classification: HYDROLASE
Organism(s): Orpinomyces sp. Y102
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-05-12 Released: 2017-05-17
Deposition Author(s): Tsai, L.C., Huang, H.C.
Funding Organization(s): NSC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.239 (Depositor), 0.250 (DCC)
R-Value Work:
0.209 (Depositor)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo- and endo- activity in a complex with cellobiose

Huang, H.C., Qi, L.H., Chen, Y.C., Tsai, L.C.

(2019) Acta Crystallogr D Biol Crystallogr

Macromolecule Content

Total Structure Weight: 144.34 kDa
Atom Count: 11,278
Modeled Residue Count: 1,288
Deposited Residue Count: 1,288
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A, B, C, D	322	Orpinomyces sp. Y102	Mutation(s): 0 Gene Names: cbhC7 EC: 3.2.1
UniProt
Find proteins for A0A076U926 (Orpinomyces sp. Y102) Explore A0A076U926 Go to UniProtKB: A0A076U926
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A076U926
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain TA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain TA [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain TA [auth D]	HA [auth C], IA [auth C], TA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain IA [auth C] Focus chain TA [auth D] Interactions & Density Focus chain HA [auth C] Focus chain IA [auth C] Focus chain TA [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain PA [auth D] SDF format, chain SA [auth D] SDF format, chain V [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain V [auth B]	CA [auth C] DA [auth C] F [auth A] G [auth A] PA [auth D] CA [auth C], DA [auth C], F [auth A], G [auth A], PA [auth D], SA [auth D], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain PA [auth D] Focus chain SA [auth D] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain PA [auth D] Focus chain SA [auth D] Focus chain V [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain U [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain I [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth A]	BA [auth B] EA [auth C] FA [auth C] GA [auth C] H [auth A] BA [auth B], EA [auth C], FA [auth C], GA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], QA [auth D], RA [auth D], U [auth A], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain OA [auth C] MOL2 format, chain OA [auth C] mmCIF format, chain OA [auth C]	OA [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain OA [auth C] Interactions & Density Focus chain OA [auth C]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain Z [auth B]	AA [auth B] JA [auth C] KA [auth C] LA [auth C] MA [auth C] AA [auth B], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], UA [auth D], VA [auth D], Z [auth B]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain AA [auth B] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.239 (Depositor), 0.250 (DCC)
R-Value Work: 0.209 (Depositor)
R-Value Observed: 0.211 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 309.859	α = 90
b = 87.353	β = 93.95
c = 82.551	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data processing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Tsai, L.C.

Huang, H.C.

Funding Organization	Location	Grant Number
NSC	Taiwan	NSC101-2311-B-027-001

Revision History (Full details and data files)

Version 1.0: 2017-05-17
Type: Initial release
Version 1.1: 2019-10-30
Changes: Data collection, Database references
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Structure summary