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- PDB-4a02: X-ray crystallographic structure of EfCBM33A -

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Basic information

Entry
Database: PDB / ID: 4a02
TitleX-ray crystallographic structure of EfCBM33A
ComponentsCHITIN BINDING PROTEIN
KeywordsCHITIN BINDING PROTEIN / CHITIN DEGRADATION / CHITIN OXIDATION
Function / homology
Function and homology information


lytic chitin monooxygenase / chitin catabolic process / chitin binding / polysaccharide catabolic process / monooxygenase activity / copper ion binding / extracellular region
Similarity search - Function
chitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
Lytic chitin monooxygenase
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsVaaje-Kolstad, G. / Bohle, L.A. / Gaseidnes, S. / Dalhus, B. / Bjoras, M. / Mathiesen, G. / Eijsink, V.G.H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Characterization of the Chitinolytic Machinery of Enterococcus Faecalis V583 and High Resolution Structure of its Oxidative Cbm33 Enzyme
Authors: Vaaje-Kolstad, G. / Bohle, L.A. / Gaseidnes, S. / Dalhus, B. / Bjoras, M. / Mathiesen, G. / Eijsink, V.G.H.
History
DepositionSep 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Other
Revision 1.2Nov 21, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHITIN BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,3391
Polymers18,3391
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.109, 52.109, 59.653
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein CHITIN BINDING PROTEIN / EFCBM33A / CBM33


Mass: 18339.301 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Strain: V582 / Plasmid: PRSET-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q838S1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.3 % / Description: NONE
Crystal growpH: 8
Details: 1.0 M K/NA TARTRATE, 0.1 M IMIDAZOLE PH 8.0 AND 0.2 M NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 0.95→23.9 Å / Num. obs: 112000 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rsym value: 0.053 / Net I/σ(I): 12.1
Reflection shellResolution: 0.95→1 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.221 / % possible all: 86.6

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BEM

2bem


Resolution: 0.95→23.9 Å / Num. parameters: 14448 / Num. restraintsaints: 17468 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1158 5601 5 %RANDOM
obs0.0964 -96 %-
all-111940 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refinement stepCycle: LAST / Resolution: 0.95→23.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 286 1586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0313
X-RAY DIFFRACTIONs_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.133
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.112

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