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- PDB-1hf6: ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMB... -

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Basic information

Entry
Database: PDB / ID: 1hf6
TitleENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMBIC CRYSTAL FORM IN COMPLEX WITH CELLOTRIOSE
ComponentsENDOGLUCANASE B
KeywordsHYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSHYDROLASE FAMILY 5
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily ...Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-cellotriose / ACETIC ACID / Endoglucanase 5A
Similarity search - Component
Biological speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsVarrot, A. / Withers, S. / Vasella, A. / Schulein, M. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Direct Experimental Observation of the Hydrogen-Bonding Network of a Glycosidase Along its Reaction Coordinate Revealed by Atomic Resolution Analyses of Endoglucanase Cel5A
Authors: Varrot, A. / Davies, G.J.
History
DepositionNov 29, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / struct_conn / 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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8436
Polymers33,9981
Non-polymers8455
Water8,485471
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.605, 69.449, 77.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: ACTIVE AS A MONOMER

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ENDOGLUCANASE B / ENDO-1 / 4-BETA-GLUCANASE / CELLULASE SYNONYM: CELLULASE / ENDO-1 / 4-BETA-GLUCANASE


Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN ONLY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Plasmid: THERMAMYL-AMYLASE PROMOT / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): PL2306 / References: UniProt: O85465, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][<C5O4>]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 475 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGIN AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGIN AT THE FIRST RESIDUE OBTAINED AFTER CLEAVAGE OF THE PROSEQUENCE

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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: 1.9 Å3/Da / Density % sol: 35.58 %
Crystal growpH: 4.6
Details: PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 100MM SODIUM CITRATE PH 5.5, 25% GLYCEROL AS CRYOPROTECTANT
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Davies, G.J., (1998) Biochemistry, 37, 1926.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8-1.2 Mammonium sulfate1reservoir
215 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.069
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.069 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / Num. obs: 102353 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 24.8
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.307 / % possible all: 93
Reflection
*PLUS
Highest resolution: 1.15 Å / Lowest resolution: 20 Å / Redundancy: 4.3 %
Reflection shell
*PLUS
% possible obs: 93 % / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A3H

3a3h


Resolution: 1.15→20 Å / SU B: 0.955 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST THREE RESIDUES WERE NOT VISIBLE IN DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.137 5175 5 %RANDOM
Rwork0.114 ---
obs0.115 98264 98.9 %-
Displacement parametersBiso mean: 9.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---0.75 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 53 471 2901
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.05

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