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- PDB-1olr: The Humicola grisea Cel12A Enzyme Structure at 1.2 A Resolution -

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Basic information

Entry
Database: PDB / ID: 1olr
TitleThe Humicola grisea Cel12A Enzyme Structure at 1.2 A Resolution
ComponentsENDO-BETA-1,4-GLUCANASE
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSYL HYDROLASE / GH FAMILY 12 / HUMICOLA GRISEA 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 speciesHUMICOLA GRISEA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 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

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Assembly

Deposited unit
A: ENDO-BETA-1,4-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)25,8891
Polymers25,8891
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.231, 49.231, 165.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2098-

HOH

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Components

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


Mass: 25888.586 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 31-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMICOLA GRISEA (fungus) / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: Q8NJY3, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 33 %
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-IDSol-IDDetails
10.02 Mcacodylate1reservoirpH6.0
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: MAX II / Beamline: I711 / Wavelength: 1.09
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 1.22→30 Å / Num. obs: 58847 / % possible obs: 95 % / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 24
Reflection shellResolution: 1.22→1.24 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4 / % possible all: 84
Reflection
*PLUS
Highest resolution: 1.22 Å / Lowest resolution: 30 Å / % possible obs: 94.6 % / Redundancy: 5.5 % / Num. measured all: 321815 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 84.4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4

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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: 1.2→30 Å / SU B: 1.30636 / SU ML: 0.03069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06672 / ESU R Free: 0.05455
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
Rfree0.15132 1793 3.1 %RANDOM
Rwork0.13455 ---
obs0.13508 56977 95.2 %-
Displacement parametersBiso mean: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 0 329 2161
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1740.5
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
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: 1.22 Å / Rfactor Rfree: 0.151 / Rfactor Rwork: 0.135
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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