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- PDB-1g0c: ALKALINE CELLULASE K CATALYTIC DOMAIN-CELLOBIOSE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1g0c
TitleALKALINE CELLULASE K CATALYTIC DOMAIN-CELLOBIOSE COMPLEX
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / Alpha/beta barrel / TIM-barrel / cellobiose complex
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily ...Carbohydrate binding module family 17/28 / Carbohydrate binding domain (family 17/28) / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellobiose / ACETIC ACID / : / Endoglucanase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsShirai, T. / Ishida, H. / Noda, J. / Yamane, T. / Ozaki, K. / Hakamada, Y. / Ito, S.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.
Authors: Shirai, T. / Ishida, H. / Noda, J. / Yamane, T. / Ozaki, K. / Hakamada, Y. / Ito, S.
History
DepositionOct 5, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,07416
Polymers40,3671
Non-polymers1,70715
Water8,539474
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.9, 97.9, 121.6
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-594-

CD

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Components

#1: Protein ENDOGLUCANASE


Mass: 40367.254 Da / Num. of mol.: 1 / Fragment: ALKALINE CELLULASE K CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: KSM-635 / Plasmid: PHSP-BC115B / Production host: Bacillus subtilis (bacteria) / References: UniProt: P19424, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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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: 4.17 Å3/Da / Density % sol: 70.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Cadmium sulfate hydrate, sodium acetate, HEPES, cellobiose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %(w/v)protein1drop
220 mMcadmium sulfate hydrate1drop
30.5 Msodium acetate1drop
40.1 MHEPES1drop
540 mMcadmium sulfate hydrate1reservoir
61.0 Msodium acetate1reservoir
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→8 Å / Num. all: 53676 / Num. obs: 47889 / % possible obs: 89.2 % / Observed criterion σ(I): 1 / Redundancy: 27.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.187 / % possible all: 72.4
Reflection
*PLUS
Lowest resolution: 40 Å / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 72.4 % / Num. unique obs: 3826 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2339 -random
Rwork0.181 ---
all-53676 --
obs-46786 87.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 49 474 3319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_torsion_deg23.5
X-RAY DIFFRACTIONx_torsion_impr_deg2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 5 % / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.242 / Num. reflection Rfree: 191 / % reflection Rfree: 5 % / Num. reflection obs: 3807 / Rfactor all: 0.24

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