5ECU | pdb_00005ecu

The unliganded structure of Caldicellulosiruptor saccharolyticus GH5

PDB DOI: https://doi.org/10.2210/pdb5ECU/pdb

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

Deposited: 2015-10-20 Released: 2016-11-02
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.115 (Depositor), 0.116 (DCC)
R-Value Work:
0.085 (Depositor), 0.086 (DCC)
R-Value Observed:
0.087 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

The structure of Caldicellulosiruptor saccharolyticus GH5

Alahuhta, P.M., Lunin, V.V.

To be published.

Macromolecule Content

Total Structure Weight: 65.57 kDa
Atom Count: 3,596
Modeled Residue Count: 350
Deposited Residue Count: 555
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulase	A	555	Caldicellulosiruptor saccharolyticus	Mutation(s): 0 Gene Names: Csac_0678 EC: 3.2.1.4
UniProt
Find proteins for A4XHB2 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XHB2 Go to UniProtKB: A4XHB2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XHB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A]	HA [auth A], IA [auth A], JA [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain BA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] 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] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] 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 U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain B [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] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] 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 U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain B [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] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] 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 U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [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], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] 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] 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 Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain B [auth A] 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] 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 Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain OA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain OA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain OA [auth A]	KA [auth A] LA [auth A] MA [auth A] NA [auth A] OA [auth A] KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Interactions & Density Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain RA [auth A] SDF format, chain SA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A]	RA [auth A], SA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain RA [auth A] Focus chain SA [auth A] Interactions & Density Focus chain RA [auth A] Focus chain SA [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.115 (Depositor), 0.116 (DCC)
R-Value Work: 0.085 (Depositor), 0.086 (DCC)
R-Value Observed: 0.087 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.66	α = 90
b = 146.66	β = 90
c = 146.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Blu-Ice	data collection
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Alahuhta, P.M.

Lunin, V.V.

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2017-02-15
Changes: Derived calculations
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description