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- PDB-1qi0: ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE TETRAGONAL... -

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Basic information

Entry
Database: PDB / ID: 1qi0
TitleENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE TETRAGONAL CRYSTAL FORM IN COMPLEX WITH CELLOBIOSE
ComponentsENDOGLUCANASE B
KeywordsHYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSHYDROLASE FAMILY 5I
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
beta-cellobiose / Endoglucanase 5A / Endoglucanase B
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.1 Å
AuthorsVarrot, A. / Schulein, M. / Davies, G.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Insights into ligand-induced conformational change in Cel5A from Bacillus agaradhaerens revealed by a catalytically active crystal form.
Authors: Varrot, A. / Schulein, M. / Davies, G.J.
History
DepositionJun 2, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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_alt_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6997
Polymers34,1561
Non-polymers5436
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: ENDOGLUCANASE B
hetero molecules

A: ENDOGLUCANASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,39814
Polymers68,3122
Non-polymers1,08512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area2050 Å2
ΔGint-98 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.710, 74.710, 136.475
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 34156.180 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus agaradhaerens (bacteria) / Strain: AC13 / Plasmid: PMOL995 / Production host: Bacillus subtilis (bacteria) / Strain (production host): PL2306 CELLULASE NEGATIVE
References: UniProt: P06565, UniProt: O85465*PLUS, 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
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 26 FIRST RESIDUES ARE CLEAVED IN ORDER TO GET THE MATURE PROTEIN. THE REAL NUMBERING BEGINS AT ...THE 26 FIRST RESIDUES ARE CLEAVED IN ORDER TO GET THE MATURE PROTEIN. THE REAL NUMBERING BEGINS AT RESIDUE 27 WHICH IS 1 IN THIS ENTRY. THE FIRST 3 RESIDUES OF THE CORE ARE TOO DISORDERED TO BE SEEN IN THE DENSITY MAP. THE CORE DOMAIN CORRESPONDS TO RESIDUES 1-305.

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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: 2.48 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 7
Details: PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 28% PEG400 AS PRECIPITANT, 100MM TRIETHANOLAMINE AT PH 7.0 AS BUFFER AND 200 MM CACL2
Crystal grow
*PLUS
Temperature: 100 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 %PEG4001reservoir
2100 mMtriehanolamine1reservoir
3200 mMcalcium chloride1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: LONG MIRRORS (MSC)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 23002 / % possible obs: 99.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 9.4 / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 5.9 / Rsym value: 29.8 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.1→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1182 5 %RANDOM
Rwork0.172 ---
obs0.168 23225 100 %-
Displacement parametersBiso mean: 21.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 28 292 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6243
X-RAY DIFFRACTIONp_mcangle_it2.1915
X-RAY DIFFRACTIONp_scbond_it2.624
X-RAY DIFFRACTIONp_scangle_it3.5826
X-RAY DIFFRACTIONp_plane_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.10.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2010.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1350.3
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor12.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.120
X-RAY DIFFRACTIONp_special_tor

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