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- PDB-1e5j: ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE TETRAGONAL... -

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Basic information

Entry
Database: PDB / ID: 1e5j
TitleENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE TETRAGONAL CRYSTAL FORM IN COMPLEX WITH METHYL-4II-S-ALPHA-CELLOBIOSYL-4II-THIO-BETA-CELLOBIOSIDE
ComponentsENDOGLUCANASE 5A
KeywordsHYDROLASE / CELLULOSE DEGRADATION / 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
Biological speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.85 Å
AuthorsFort, S. / Varrot, A. / Schulein, M. / Cottaz, S. / Driguez, H. / Davies, G.J.
CitationJournal: Chembiochem / Year: 2001
Title: Mixed-Linkage Cellooligosaccharides: A New Class of Glycoside Hydrolase Inhibitors
Authors: Fort, S. / Varrot, A. / Schulein, M. / Cottaz, S. / Driguez, H. / Davies, G.J.
History
DepositionJul 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _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_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_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.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 2.1May 8, 2024Group: 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 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0296
Polymers34,1561
Non-polymers8735
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.520, 74.520, 136.193
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 5A / CELLULASE / ENDO-1 / 4-BETA-GLUCANASE / ALKALINE CELLULASE / ENDO-1 / 4-BETA-GLUCANASE 5A


Mass: 34156.180 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) / Strain: AC13 / Plasmid: THERMAMYL-AMYLASE PROMOT / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): PL2306 / References: UniProt: O85465, cellulase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)- ...alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 712.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-3/a4-b1_b4-c1*S*_c4-d1*S*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][a-D-Glcp4SH]{[(4+S)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE. SIMILARITY: ...CATALYTIC ACTIVITY: ENDOHYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE. SIMILARITY: BELONGS TO CELLULASE FAMILY A (FAMILY 5 OF GLYCOSYL HYDROLASES).
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 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
Temperature: 100 K / pH: 7 / Method: vapor diffusion, hanging drop / Details: Varrot, A., (2000) J.Mol.Biol., 279, 819.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
228 %PEG4001reservoir
3100 mMtriethanolamine1reservoir
4200 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 2000 / 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: 1.85→15 Å / Num. obs: 32666 / % possible obs: 98.7 % / Redundancy: 3 % / Biso Wilson estimate: 23.32 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 19.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.265 / % possible all: 96.5
Reflection
*PLUS
Lowest resolution: 15 Å / Redundancy: 3 %
Reflection shell
*PLUS
% possible obs: 96.5 % / Redundancy: 3 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.85→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1676 5 %RANDOM
Rwork0.177 ---
obs0.179 31361 98.7 %-
Displacement parametersBiso mean: 23.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 50 328 2766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.5
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3453
X-RAY DIFFRACTIONp_mcangle_it2.9655
X-RAY DIFFRACTIONp_scbond_it3.3314
X-RAY DIFFRACTIONp_scangle_it4.2466
X-RAY DIFFRACTIONp_plane_restr0.0250.03
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2480.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor11.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177 / Rfactor Rfree: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.023

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