2CIP | pdb_00002cip

Structure of the Michaelis complex of a family 26 lichenase

PDB DOI: https://doi.org/10.2210/pdb2CIP/pdb

Classification: HYDROLASE
Organism(s): Acetivibrio thermocellus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-03-24 Released: 2006-07-12
Deposition Author(s): Money, V.A., Smith, N.L., Scaffidi, A., Stick, R.V., Gilbert, H.J., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.179 (Depositor), 0.186 (DCC)
R-Value Work:
0.152 (Depositor)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Substrate Distortion by a Lichenase Highlights the Different Conformational Itineraries Harnessed by Related Glycoside Hydrolases.

Money, V.A., Smith, N.L., Scaffidi, A., Stick, R.V., Gilbert, H.J., Davies, G.J.

(2006) Angew Chem Int Ed Engl 45: 5136

PubMed: 16823793 Search on PubMed
DOI: https://doi.org/10.1002/anie.200600802
Primary Citation Related Structures:
2CIP, 2CIT

Organizational Affiliation

York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK.

Macromolecule Content

Total Structure Weight: 32.62 kDa
Atom Count: 2,812
Modeled Residue Count: 273
Deposited Residue Count: 282
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE H	A	282	Acetivibrio thermocellus	Mutation(s): 1 EC: 3.2.1.4
UniProt
Find proteins for P16218 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore P16218 Go to UniProtKB: P16218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16218
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B	2		N/A	Interactions Focus chain B
Glycosylation Resources
GlyTouCan: G36535HU GlyCosmos: G36535HU

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZZ1 Query on ZZ1 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-METHYL-2H-CHROMEN-2-ONE C₁₀ H₈ O₂ PSGQCCSGKGJLRL-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900024 Query on PRD_900024	B	beta-laminaribiose	Oligosaccharide / Antimicrobial		Interactions Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.179 (Depositor), 0.186 (DCC)
R-Value Work: 0.152 (Depositor)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.747	α = 90
b = 63.167	β = 90
c = 78.756	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-07-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-07-12
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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-05-08
Changes: Data collection, Database references, Structure summary