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- PDB-1oa3: Comparison of Family 12 Glycoside Hydrolases and Recruited Substi... -

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Basic information

Entry
Database: PDB / ID: 1oa3
TitleComparison of Family 12 Glycoside Hydrolases and Recruited Substitutions Important for Thermal Stability
ComponentsENDO-BETA-1-4-GLUCANASE
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSYL HYDROLASE / GH FAMILY 12 / HYPOCREA SCHWEINITZII CEL12A
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHYPOCREA SCHWEINITZII (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSandgren, M. / Gualfetti, P.J. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Day, A.G. / Jones, T.A. / Mitchinson, C.
CitationJournal: Protein Sci. / Year: 2003
Title: Comparison of Family 12 Glycoside Hydrolases and Recruited Substitutions Important for Thermal Stability
Authors: Sandgren, M. / Gualfetti, P.J. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Day, A.G. / Jones, T.A. / Mitchinson, C.
History
DepositionDec 28, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-BETA-1-4-GLUCANASE
B: ENDO-BETA-1-4-GLUCANASE
C: ENDO-BETA-1-4-GLUCANASE
D: ENDO-BETA-1-4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8468
Polymers93,9614
Non-polymers8854
Water10,737596
1
A: ENDO-BETA-1-4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7122
Polymers23,4901
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENDO-BETA-1-4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7122
Polymers23,4901
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ENDO-BETA-1-4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7122
Polymers23,4901
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ENDO-BETA-1-4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7122
Polymers23,4901
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.490, 77.547, 83.410
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENDO-BETA-1-4-GLUCANASE / ENDOGLUCANASE / CEL12A


Mass: 23490.371 Da / Num. of mol.: 4 / Fragment: RESIDUES 17-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HYPOCREA SCHWEINITZII (fungus) / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: Q8NJY6, cellulase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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 Å3/Da / Density % sol: 40 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 20-24 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1200 mMcacodylate1reservoirpH6.0
2200 mMammonium acetate1reservoir
310-30 %(w/w)PEG2000MME1reservoir
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 85680 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rsym value: 0.097 / Net I/σ(I): 14
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 5.7 / Rsym value: 0.12 / % possible all: 84.6
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. obs: 85680 / % possible obs: 98.9 % / Redundancy: 4 % / Num. measured all: 346287 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.73 Å / % possible obs: 84.6 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 5.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8V

1h8v


Resolution: 1.7→29 Å / SU B: 2.62733 / SU ML: 0.08854 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22478 / ESU R Free: 0.1567 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21653 2573 3 %RANDOM
Rwork0.19197 ---
obs0.1927 83042 98.9 %-
Displacement parametersBiso mean: 9.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.34 Å2
2--0.21 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 56 596 7300
Refinement
*PLUS
Highest resolution: 1.7 Å / Num. reflection obs: 83042 / Num. reflection Rfree: 2573 / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3

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