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- PDB-1h2j: ENDOGLUCANASE CEL5A IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY L... -

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Basic information

Entry
Database: PDB / ID: 1h2j
TitleENDOGLUCANASE CEL5A IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY LINKED 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-CELLOBIOSIDE AT 1.15 A RESOLUTION
ComponentsENDOGLUCANASE 5A
KeywordsHYDROLASE / GLYCOSIDASE / ENDOGLUCANASE
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
Chem-DCB / Endoglucanase 5A
Similarity search - Component
Biological speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsVarrot, A. / 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
SupersessionAug 9, 2002ID: 1HF7
DepositionAug 9, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Dec 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7895
Polymers33,9981
Non-polymers7914
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.355, 69.572, 77.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENDOGLUCANASE 5A / ENDO-1 / 4-BETA-GLUCANASE / ALKALINE CELLULASE / CEL5A


Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Strain: AC13 / Plasmid: THERMAMYL-AMYLASE PROMOTOR / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): PL2306 / References: UniProt: O85465, cellulase
#2: Chemical ChemComp-DCB / 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-D-CELLOBIOSIDE / 2',4'-DINITROPHENYL-2DEOXY-2-FLURO-B-D-CELLOBIOSIDE


Mass: 510.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23FN2O14
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMEMBER OF THE CELLULASE FAMILY OF GLYCOSYL HYDROLASES
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. ONLY THE CATALYTIC DOMAIN HAS CRYSTALLISED. THIS CORRESPOND TO RESIDUES 27 TO 329 IN THE DATABASE. THE FIRST 3 RESIDUES ARE NOT VISIBLE IN ELECTRON DENSITY. A THIRD CONFORMATION HAS BEEN BUILT FOR GLU 228. THE A CONFORMER IS THE ONE OBERVED IN THE MICKAELIS FORM.THE B AND C CONFORMERS ARE PART OF THE COVALENT INTERMEDIATE FORM. TYR 202 SOULD ALSO BE IN 3 CONFORMATIONS TO AVOID CLASHES WITH GLU 228 BUT IT COULD NOT BE BUILT DUE TO DISORDER

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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, 25% GLYCEROL AS CRYOPROTECTANT, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8445
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8445 Å / Relative weight: 1
ReflectionResolution: 1.15→40 Å / Num. obs: 103556 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.3
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A3H USED AS STARTING MODEL WITHOUT WATER AND SUBSTRATE

4a3h


Resolution: 1.15→40 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.392 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.136 5206 5 %RANDOM
Rwork0.117 ---
obs0.118 98396 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---0.78 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 52 378 2807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212594
X-RAY DIFFRACTIONr_bond_other_d0.0010.022127
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9463547
X-RAY DIFFRACTIONr_angle_other_deg2.06634985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022891
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02498
X-RAY DIFFRACTIONr_nbd_refined0.220.2556
X-RAY DIFFRACTIONr_nbd_other0.2690.22509
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21286
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3260.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5431.51511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.22222448
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.79431083
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.024.51094
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.64522594
X-RAY DIFFRACTIONr_sphericity_free5.5342378
X-RAY DIFFRACTIONr_sphericity_bonded3.99122524
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.174 372
Rwork0.174 7206

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