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- PDB-1tvn: Cellulase cel5G from Pseudoalteromonas haloplanktis, A family GH ... -

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Basic information

Entry
Database: PDB / ID: 1tvn
TitleCellulase cel5G from Pseudoalteromonas haloplanktis, A family GH 5-2 enzyme
Componentscellulase
KeywordsHYDROLASE / Glycoside hydrolase / Clan GH-A / Family 5-2 / Cellulase
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide catabolic process / carbohydrate binding / cell adhesion / calcium ion binding / extracellular region
Similarity search - Function
Endoglucanase Z, cellulose-binding domain / Cellulose-binding domain / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / 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. ...Endoglucanase Z, cellulose-binding domain / Cellulose-binding domain / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / 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 speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsViolot, S. / Haser, R. / Aghajari, N.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structure of a Full Length Psychrophilic Cellulase from Pseudoalteromonas haloplanktis revealed by X-ray Diffraction and Small Angle X-ray Scattering
Authors: Violot, S. / Aghajari, N. / Czjzek, M. / Feller, G. / Sonan, G.K. / Gouet, P. / Gerday, C. / Haser, R. / Receveur-Brechot, V.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Expression, purification, crystallization and preliminary X-ray crystallographic studies of a psychrophilic cellulase from Pseudoalteromonas haloplanktis
Authors: Violot, S. / Haser, R. / Sonan, G. / Georlette, D. / Feller, G. / Aghajari, N.
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cellulase
B: cellulase


Theoretical massNumber of molelcules
Total (without water)63,8302
Polymers63,8302
Non-polymers00
Water13,980776
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.400, 78.900, 44.100
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 cellulase / Endoglucanase G


Mass: 31914.918 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria)
Gene: celG / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurian BL21 (DE3) / References: UniProt: O86099, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.3M tri-sodium citrate dihydrate, 40% (v/v) glycerol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9559 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 30, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9559 Å / Relative weight: 1
ReflectionResolution: 1.41→14.008 Å / Num. all: 209086 / Num. obs: 87830 / % possible obs: 95.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.043
Reflection shellResolution: 1.41→1.48 Å / Redundancy: 1.8 % / Num. unique all: 9973 / Rsym value: 0.175 / % possible all: 75.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EGZ

1egz


Resolution: 1.41→13.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1740239.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.177 4426 5 %RANDOM
Rwork0.15 ---
obs0.15 87749 94.8 %-
all-209086 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.2331 Å2 / ksol: 0.392917 e/Å3
Displacement parametersBiso mean: 11.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---1.45 Å20 Å2
3---1.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.41→13.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 0 776 5361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.61
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.312.5
LS refinement shellResolution: 1.41→1.49 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 549 5.2 %
Rwork0.213 10103 -
obs--68.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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