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- PDB-1h8v: The X-ray Crystal Structure of the Trichoderma reesei Family 12 E... -

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Basic information

Entry
Database: PDB / ID: 1h8v
TitleThe X-ray Crystal Structure of the Trichoderma reesei Family 12 Endoglucanase 3, Cel12A, at 1.9 A Resolution
ComponentsENDO-BETA-1,4-GLUCANASE
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / GH FAMILY 12 / GLYCOSYL HYDROLASE
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 / MIR / Resolution: 1.9 Å
AuthorsSandgren, M. / Shaw, A. / Ropp, T.H. / Wu, S. / Bott, R. / Cameron, A.D. / Stahlberg, J. / Mitchinson, C. / Jones, T.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The X-Ray Crystal Structure of the Trichoderma Reesei Family 12 Endoglucanase 3, Cel12A, at 1.9 A Resolution
Authors: Sandgren, M. / Shaw, A. / Ropp, T.H. / Wu, S. / Bott, R. / Cameron, A.D. / Stahlberg, J. / Mitchinson, C. / Jones, T.A.
History
DepositionFeb 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / 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

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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
E: ENDO-BETA-1,4-GLUCANASE
F: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,16712
Polymers140,8406
Non-polymers1,3276
Water21,2221178
1
A: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,4731
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)23,6952
Polymers23,4731
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,4731
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,4731
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,4731
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6952
Polymers23,4731
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.720, 71.580, 121.400
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99422, 0.01522, -0.10629), (0.01604, 0.99985, -0.00683), (0.10617, -0.0085, -0.99431)72.05952, -3.64691, 53.76633
2given(-0.99824, -0.0187, -0.05622), (-0.04465, -0.38643, 0.92124), (-0.03895, 0.92213, 0.38492)93.66165, 14.688, -2.77647
3given(0.99677, 0.02344, 0.07683), (-0.04729, -0.60189, 0.79718), (0.06493, -0.79824, -0.59883)-26.69941, 24.68633, 70.67968
4given(-0.99642, 0.04755, -0.06989), (0.03279, -0.54463, -0.83803), (-0.07791, -0.83732, 0.54113)116.01016, 67.32108, 41.98259
5given(0.99701, -0.05577, 0.05353), (0.01272, -0.56463, -0.82525), (0.07624, 0.82346, -0.56223)22.2889, 64.897, 18.86832

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Components

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


Mass: 23473.342 Da / Num. of mol.: 6 / Fragment: RESIDUES 17-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Production host: TRICHODERMA REESEI (fungus) / References: UniProt: O00095, cellulase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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 / Water


Mass: 18.015 Da / Num. of mol.: 1178 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE
Sequence detailsGLN 17 MODIFIED RESIDUE

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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-ID
115 mg/mlprotein1drop
2200 mMcacodylate1reservoir
3200 mMammonium acetate1reservoir
410-30 %(w/w)mPEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: MIRRIRS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29 Å / Num. obs: 87132 / % possible obs: 92 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 5.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4 / % possible all: 84.5
Reflection
*PLUS
Num. measured all: 230270
Reflection shell
*PLUS
% possible obs: 84.5 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→28.1 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2571 3 %RANDOM
Rwork0.189 ---
obs0.189 86852 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.22 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-1.42 Å2
2---0.92 Å20 Å2
3---1.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9966 0 84 1178 11228
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 405 2 %
Rwork0.209 13622 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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