6K54 | pdb_00006k54

Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with trisaccharide

PDB DOI: https://doi.org/10.2210/pdb6K54/pdb

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

Deposited: 2019-05-28 Released: 2020-06-03
Deposition Author(s): Baba, S., Takeda, M., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.201 (Depositor), 0.201 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Novel hyperthermophilic cellobiohydrolase II isolated from hot spring microbial community

Takeda, M., Baba, S., Okuma, J., Hirose, Y., Nishimura, A., Takata, M., Oda, K., Shibata, D., Kondo, Y., Kumasaka, T.

To be published.

Macromolecule Content

Total Structure Weight: 144.54 kDa
Atom Count: 11,798
Modeled Residue Count: 1,284
Deposited Residue Count: 1,284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH6 cellobiohydrolase, HMCEL6A	A, B, C	428	metagenome	Mutation(s): 0 EC: 3.2.1.91

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D	4		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G41724ZD GlyCosmos: G41724ZD GlyGen: G41724ZD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E, F, G	3		N/A	Interactions Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain E Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G14338VK GlyCosmos: G14338VK GlyGen: G14338VK

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE4 Query on PE4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [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 L [auth A] Interactions & Density Focus chain L [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain M [auth A]	M [auth A], U [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain M [auth A] Focus chain U [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A], Z [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth C] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] S [auth B] T [auth B] X [auth C] J [auth A], K [auth A], S [auth B], T [auth B], X [auth C], Y [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain X [auth C] Focus chain Y [auth C]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] P [auth B] Q [auth B] R [auth B] H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900021 Query on PRD_900021	E, F, G	beta-cellotriose	Oligosaccharide / Metabolism		Interactions Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain E Focus chain F Focus chain G

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.201 (Depositor), 0.201 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.582	α = 90
b = 138.699	β = 101.99
c = 110.636	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary