2CKS | pdb_00002cks

X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THERMOBIFIDA FUSCA ENDOGLUCANASE CEL5A (E5)

PDB DOI: https://doi.org/10.2210/pdb2CKS/pdb

Classification: HYDROLASE
Organism(s): Thermobifida fusca
Expression System: Bacillus subtilis
Mutation(s): No

Deposited: 2006-04-21 Released: 2007-05-29
Deposition Author(s): Berglund, G.I., Gualfetti, P.J., Requadt, C., Gross, L.S., Bergfors, T., Shaw, A., Saldajeno, M., Mitchinson, C., Sandgren, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.169 (Depositor), 0.180 (DCC)
R-Value Work:
0.142 (Depositor), 0.154 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

The Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase Cel5A in Complex with Cellotetraose

Berglund, G.I., Gualfetti, P.J., Requadt, C., Gross, L.S., Bergfors, T., Shaw, A., Saldajeno, M., Mitchinson, C., Sandgren, M.

To be published.

Macromolecule Content

Total Structure Weight: 69.21 kDa
Atom Count: 5,828
Modeled Residue Count: 611
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE E-5	A, B	306	Thermobifida fusca	Mutation(s): 0 EC: 3.2.1.4
UniProt
Find proteins for Q01786 (Thermobifida fusca) Explore Q01786 Go to UniProtKB: Q01786
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01786
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], J [auth B]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] K [auth B] D [auth A], E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], O [auth B], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.169 (Depositor), 0.180 (DCC)
R-Value Work: 0.142 (Depositor), 0.154 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.888	α = 90
b = 70.97	β = 94.05
c = 75.624	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-29
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2018-12-19
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2019-05-08
Changes: Data collection, Experimental preparation
Version 2.2: 2024-05-01
Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
Version 2.3: 2024-10-09
Changes: Structure summary