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- PDB-1egz: CELLULASE CEL5 FROM ERWINIA CHRYSANTHEMI, A FAMILY GH 5-2 ENZYME -

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Basic information

Entry
Database: PDB / ID: 1egz
TitleCELLULASE CEL5 FROM ERWINIA CHRYSANTHEMI, A FAMILY GH 5-2 ENZYME
ComponentsENDOGLUCANASE Z
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / CLAN GH-A / FAMILY 5-2 / CELLULASE
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Endoglucanase Z, cellulose-binding domain / Cellulose-binding domain / 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 ...Endoglucanase Z, cellulose-binding domain / Cellulose-binding domain / 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 speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCzjzek, M. / El Hassouni, M. / Py, B. / Barras, F.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Type II protein secretion in gram-negative pathogenic bacteria: the study of the structure/secretion relationships of the cellulase Cel5 (formerly EGZ) from Erwinia chrysanthemi
Authors: Chapon, M. / Czjzek, M. / El Hassouni, M. / Py, B. / Juy, M. / Barras, F.
History
DepositionMar 18, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 26, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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.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.value / _struct_conn.pdbx_dist_value / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE Z
B: ENDOGLUCANASE Z
C: ENDOGLUCANASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5246
Polymers96,4043
Non-polymers1203
Water5,999333
1
A: ENDOGLUCANASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1752
Polymers32,1351
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDOGLUCANASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1752
Polymers32,1351
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ENDOGLUCANASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1752
Polymers32,1351
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.800, 47.200, 120.100
Angle α, β, γ (deg.)90.00, 105.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.13187, -0.03228, 0.99074), (0.43686, 0.89528, 0.08732), (-0.88981, 0.44433, -0.10396)-111.24346, -29.71191, 25.89464
2given(-0.85794, -0.51297, -0.02815), (0.51364, -0.85539, -0.06695), (0.01027, -0.0719, 0.99736)37.33757, 33.30179, -40.37063

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Components

#1: Protein ENDOGLUCANASE Z / E.C.3.2.1.4 / EGZ / CEL5


Mass: 32134.514 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Details: GENE: CELZ / Source: (natural) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Cellular location: EXTERIOR / Secretion: TYPE II / References: UniProt: P07103, cellulase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSECRETED (MATURE) PROTEIN, CONSISTING ONLY OF THE CATALYTIC DOMAIN

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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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: VAPOR DIFFUSION HANGING DROP; PEG 4000 28%, TRIS PH 8.0 20 MM, MGSO4 20 MM, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
328 %(w/v)PEG40001reservoir
420 mMTris-HCl1reservoir
520 mM1reservoirMgSO4

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995
RadiationMonochromator: GRAPHITE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29 Å / Num. obs: 38365 / % possible obs: 98 % / Redundancy: 2.8 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.134 / Net I/σ(I): 5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.45 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 98 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 97 % / Num. unique obs: 1749 / Rmerge(I) obs: 0.373

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A3H

1a3h


Resolution: 2.3→29 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1616 4 %RANDOM
Rwork0.179 ---
obs-33555 81.5 %-
Displacement parametersBiso mean: 22.4 Å2
Refine analyzeLuzzati d res low obs: 29 Å
Refinement stepCycle: LAST / Resolution: 2.3→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6806 0 3 333 7142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.322 171 3.6 %
Rwork0.261 3141 -
obs--69.2 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Refinement
*PLUS
Num. reflection obs: 32807 / Rfactor obs: 0.187 / Rfactor Rfree: 0.226 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor obs: 0.261

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