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- PDB-1h5v: Thiopentasaccharide complex of the endoglucanase Cel5A from Bacil... -

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Basic information

Entry
Database: PDB / ID: 1h5v
TitleThiopentasaccharide complex of the endoglucanase Cel5A from Bacillus agaradharens at 1.1 A resolution in the tetragonal crystal form
ComponentsENDOGLUCANASE 5A
KeywordsHYDROLASE / CELLULASE / ENDOGLUCANASE / THIOOLIGOSACCHARIDE
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
Biological speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsVarrot, A. / Sulzenbacher, G. / Schulein, M. / Driguez, H. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Atomic Resolution Structure of Endoglucanase Cel5A in Complex with Methyl 4,4II,4III,4Iv-Tetrathio-Alpha-Cellopentoside Highlights the Alternative Binding Modes Targeted by Substrate Mimics
Authors: Varrot, A. / Schulein, M. / Fruchard, S. / Driguez, H. / Davies, G.J.
History
DepositionMay 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: 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: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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_alt_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_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _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_conn_type.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

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Assembly

Deposited unit
A: ENDOGLUCANASE 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,48814
Polymers34,1181
Non-polymers1,37013
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.169, 75.169, 135.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2061-

HOH

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Components

#1: Protein ENDOGLUCANASE 5A / ENDO-1 / 4-BETA-GLUCANASE / CELLULASE


Mass: 34118.168 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN RESIDUES 27-331
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 alpha-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)- ...alpha-D-glucopyranose-(1-4)-1,4-dithio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl 4-thio-alpha-D-glucopyranoside


Type: oligosaccharide / Mass: 923.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[a2122h-1a_1-5_1*OC][a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-3/a4-b1*S*_b4-c1*S*_c4-d1*S*_d4-e1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Glcp4SH]{[(4+S)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE FIRST RESIDUE OBTAINED AFTER CLEAVAGE OF THE PROSEQUENCE. RESIDUES ASP A 3 AND TYR A 3 ARE SEQUENCE CONFLICTS BUT SEQADV RECORDS ARE NOT GIVEN BECAUSE THESE RESIDUES ARE UNOBSERVED.

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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: 2.73 Å3/Da / Density % sol: 54.6 %
Crystal growpH: 7
Details: PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 28% PEG400 AS PRECIPITANT, 100MM HEPES AT PH 7.0 AS BUFFER AND 200 MM CACL2. THE PROTEIN WAS INCUBATED WITH THE 1MM OF SUBSTRATE FOR AN HOUR PRIOR TO COCRYSTALLISATIOM
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
128-30 %(v/v)PEG4001reservoir
2100 mMtri-ethanolamine1reservoiror HEPES pH7.0
3200 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDetector: CCD / Date: Mar 15, 2000 / Details: TORROIDAL MIRROR
RadiationMonochromator: DIAMOND(111)GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 155682 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.6
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 4.2 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Redundancy: 3.6 %
Reflection shell
*PLUS
% possible obs: 98.7 % / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QHZ

1qhz


Resolution: 1.1→20 Å / SU B: 0.72227 / SU ML: 0.01778 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.03223 / Details: THE FIRST THREE RESIDUES DUE TO DISORD
RfactorNum. reflection% reflectionSelection details
Rfree0.13805 7867 5 %RANDOM
Rwork0.12002 ---
obs0.12093 148418 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 69 537 2988
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.12 / Rfactor Rfree: 0.138 / Rfactor Rwork: 0.12
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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