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- PDB-1oa4: Comparison of Family 12 Glycoside Hydrolases and Recruited Substi... -

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Basic information

Entry
Database: PDB / ID: 1oa4
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 / STREPTOMYCES SP 11AG8 CEL12A
Function / homology
Function and homology information


cellulase activity / polysaccharide binding / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily ...Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSTREPTOMYCES SP. 11AG8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 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)23,8901
Polymers23,8901
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.160, 54.630, 62.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23890.135 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 32-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES SP. 11AG8 (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / References: UniProt: Q9KIH1, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 %(w/w)PEG5000 MME1reservoir
2200 mMsodium cacodylate1reservoirpH5.0-6.0
315 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MSC / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→29 Å / Num. obs: 26559 / % possible obs: 73 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Rsym value: 0.054 / Net I/σ(I): 15.4
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 8.6 / Rsym value: 0.161 / % possible all: 63.5
Reflection
*PLUS
Lowest resolution: 29 Å / % possible obs: 72.9 % / Redundancy: 3.3 % / Num. measured all: 88448 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 63.5 % / Rmerge(I) obs: 0.161

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Processing

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

1nlr


Resolution: 1.5→29 Å / SU B: 2.08226 / SU ML: 0.07506 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16547 / ESU R Free: 0.1227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19264 821 3.1 %RANDOM
Rwork0.18149 ---
obs0.18185 25464 72.1 %-
Displacement parametersBiso mean: 14.276 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 0 117 1802
Refinement
*PLUS
Rfactor Rfree: 0.193 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.0119
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

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