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- PDB-1olq: The Trichoderma reesei cel12a P201C mutant, structure at 1.7 A re... -

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Basic information

Entry
Database: PDB / ID: 1olq
TitleThe Trichoderma reesei cel12a P201C mutant, structure at 1.7 A resolution
ComponentsENDO-BETA-1,4-GLUCANASE
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSYL HYDROLASE / GH FAMILY 12
Function / homology
Function and homology information


cellulase / 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 speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSandgren, M. / Gualfetti, P.J. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Berglund, G.I. / Jones, T.A. / Mitchinson, C.
CitationJournal: Protein Sci. / Year: 2003
Title: The Humicola Grisea Cel12A Enzyme Structure at 1.2 A Resolution and the Impact of its Free Cysteine Residues on Thermal Stability
Authors: Sandgren, M. / Gualfetti, P.J. / Paech, C. / Paech, S. / Shaw, A. / Gross, L.S. / Saldajeno, M. / Berglund, G.I. / Jones, T.A. / Mitchinson, C.
History
DepositionAug 11, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / 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 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4014
Polymers46,9592
Non-polymers4422
Water5,170287
1
A: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7012
Polymers23,4791
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7012
Polymers23,4791
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.616, 70.616, 69.092
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein ENDO-BETA-1,4-GLUCANASE / ENDOGLUCANASE / CEL12A / EG3


Mass: 23479.369 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-234 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: O00095, 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.: 2
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.: 287 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION PRO217CYS ENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE
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 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetailsSol-ID
10.02 Mcacodylate1pH6.0reservoir
20.02 Mcalcium acetate1reservoir
310-30 %(w/w)PEG2000 MME1reservoir
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 40983 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 99.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. obs: 42832 / % possible obs: 99.8 % / Redundancy: 4.3 % / Num. measured all: 184371 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.8

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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→20 Å / SU B: 4.26607 / SU ML: 0.14491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24664 / ESU R Free: 0.18176
Details: BABINET'S PRINCIPLE FOR SCALING HAS BEEN USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIO BULK SOLVENT MODELLING. PARAMETERS FOR MASK CALCULATION THE FOLLOWING REFINEMENT PARAMETERS ARE ...Details: BABINET'S PRINCIPLE FOR SCALING HAS BEEN USED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIO BULK SOLVENT MODELLING. PARAMETERS FOR MASK CALCULATION THE FOLLOWING REFINEMENT PARAMETERS ARE NOT REPRESENTED IN THE ABOVE TEMPLATE FOR REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.25107 1331 3.1 %RANDOM
Rwork0.20908 ---
obs0.21035 40983 99.9 %-
Displacement parametersBiso mean: 13.208 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 28 287 3635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1770.5
X-RAY DIFFRACTIONp_mcbond_it0.8081.5
X-RAY DIFFRACTIONp_mcangle_it1.342
X-RAY DIFFRACTIONp_scbond_it2.0853
X-RAY DIFFRACTIONp_scangle_it2.8314.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.7 Å / Num. reflection obs: 40981 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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