4JS7 | pdb_00004js7

Crystal structure of D78N mutant apo form of clavibacter michiganensis expansin

PDB DOI: https://doi.org/10.2210/pdb4JS7/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Clavibacter michiganensis subsp. michiganensis NCPPB 382
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-03-22 Released: 2014-03-26
Deposition Author(s): Yennawar, N.H., Yennawar, H.P., Georgelis, N., Cosgrove, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.176 (Depositor), 0.181 (DCC)
R-Value Work:
0.152 (Depositor), 0.156 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of wild type and d78n mutant Clavibacter michiganensis expansin, in apo form and in complex with oligosaccharides

Yennawar, N.H., Yennawar, H.P., Georgelis, N., Cosgrove, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 21.89 kDa
Atom Count: 1,828
Modeled Residue Count: 202
Deposited Residue Count: 202
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cellulose binding protein	A	202	Clavibacter michiganensis subsp. michiganensis NCPPB 382	Mutation(s): 1 Gene Names: celA, pCM1_0020 EC: 3.2.1.4
UniProt
Find proteins for A5CLK3 (Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382)) Explore A5CLK3 Go to UniProtKB: A5CLK3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5CLK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.176 (Depositor), 0.181 (DCC)
R-Value Work: 0.152 (Depositor), 0.156 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.758	α = 90
b = 69.556	β = 90
c = 81.04	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2015-10-21
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.