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- PDB-1qhz: NATIVE TETRAGONAL STRUCTURE OF THE ENDOGLUCANASE CEL5A FROM BACIL... -

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Basic information

Entry
Database: PDB / ID: 1qhz
TitleNATIVE TETRAGONAL STRUCTURE OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS
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
Endoglucanase 5A / Endoglucanase B
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.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_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

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Assembly

Deposited unit
A: ENDOGLUCANASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3977
Polymers34,1561
Non-polymers2406
Water6,161342
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)68,79314
Polymers68,3122
Non-polymers48112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area1230 Å2
ΔGint-106 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.540, 74.540, 135.930
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 ONLY
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CORRESPONDS TO THE PRECURSOR SEQUENCE OF CEL5A. THE 26 FIRST RESIDUES ARE CLEAVED SO ...THE SEQUENCE CORRESPONDS TO THE PRECURSOR SEQUENCE OF CEL5A. THE 26 FIRST RESIDUES ARE CLEAVED SO THE NUMBERING BEGINS WITH RESIDUE 27 WHICH IS 1 IN THIS ENTRY. 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / 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: 1.95→15 Å / Num. obs: 28709 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 6.8 / Net I/σ(I): 31.15
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 7.7 / Rsym value: 31.1 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A3H

1a3h


Resolution: 1.95→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1460 5 %RANDOM
Rwork0.172 ---
obs0.172 28636 100 %-
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 6 342 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
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_it1.6763
X-RAY DIFFRACTIONp_mcangle_it2.1825
X-RAY DIFFRACTIONp_scbond_it2.4224
X-RAY DIFFRACTIONp_scangle_it3.4216
X-RAY DIFFRACTIONp_plane_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.1010.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.1990.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1220.3
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor12.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.720
X-RAY DIFFRACTIONp_special_tor

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