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- PDB-1g01: ALKALINE CELLULASE K CATALYTIC DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1g01
TitleALKALINE CELLULASE K CATALYTIC DOMAIN
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / Alpha/beta barrel / TIM barrel
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) ...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
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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,79216
Polymers40,3671
Non-polymers1,42415
Water8,377465
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.2, 98.2, 122.0
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-593-

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: Chemical
ChemComp-CD / CADMIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 465 / 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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: cadmium sulfate hydrate, sodium acetate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
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: Feb 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: 54119 / Num. obs: 49176 / % possible obs: 90.9 % / Observed criterion σ(I): 1 / Redundancy: 11.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.202 / % possible all: 83.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å
Reflection shell
*PLUS
% possible obs: 83.8 % / Num. unique obs: 4496 / Mean I/σ(I) obs: 5.9

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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. reflectionSelection details
Rfree0.227 2422 random
Rwork0.196 --
all-54119 -
obs-48446 -
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 30 465 3286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_torsion_deg23
X-RAY DIFFRACTIONx_torsion_impr_deg1
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: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.274 / Num. reflection Rfree: 214 / % reflection Rfree: 5 % / Num. reflection obs: 4493 / Rfactor all: 0.264

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