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- PDB-1oa9: Structure of Melanocarpus albomyces endoglucanase -

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Basic information

Entry
Database: PDB / ID: 1oa9
TitleStructure of Melanocarpus albomyces endoglucanase
ComponentsCELLULASE
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASES
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 45 / : / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMELANOCARPUS ALBOMYCES (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHirvonen, M. / Papageorgiou, A.C.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Family 45 Endoglucanase from Melanocarpus Albomyces: Mechanistic Implications Based on the Free and Cellobiose-Bound Forms
Authors: Hirvonen, M. / Papageorgiou, A.C.
History
DepositionJan 4, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULASE


Theoretical massNumber of molelcules
Total (without water)22,9321
Polymers22,9321
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.304, 47.304, 177.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CELLULASE / ENDOGLUCANASE


Mass: 22932.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MELANOCARPUS ALBOMYCES (fungus) / References: UniProt: Q8J0K8, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.6 / Details: PEG 4000 15% W/V, 0.15 M KOAC, 0.1 M NAOAC PH 4.6
Crystal grow
*PLUS
Method: unknown / Details: Hirvonen, M., (2002) Acta Cryst., D58, 336.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8499
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8499 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 296601 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 22.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8
Reflection shellResolution: 2→2.06 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.5 / % possible all: 87.4
Reflection
*PLUS
Num. obs: 13270 / Num. measured all: 296601
Reflection shell
*PLUS
% possible obs: 87.4 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ENG

3eng


Resolution: 2→45.71 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1605776.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 624 4.7 %RANDOM
Rwork0.215 ---
obs0.215 13191 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.291 Å2 / ksol: 0.387333 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.11 Å20 Å20 Å2
2---5.11 Å20 Å2
3---10.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 0 152 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.422
X-RAY DIFFRACTIONc_scbond_it1.372
X-RAY DIFFRACTIONc_scangle_it1.962.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 104 5.1 %
Rwork0.286 1927 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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