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- PDB-1tvp: Endoglucanase cel5G from Pseudoalteromonas haloplanktis in comple... -

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Basic information

Entry
Database: PDB / ID: 1tvp
TitleEndoglucanase cel5G from Pseudoalteromonas haloplanktis in complex with cellobiose
Componentscellulase
KeywordsHYDROLASE / Glycoside hydrolase / Clan GH-A / family 5-2 / cellulase / Cellobiose complex
Function / homology
Function and homology information


cellulase / cellulase activity / carbohydrate binding / cell adhesion / carbohydrate metabolic process / 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
beta-cellobiose / Cellulase
Similarity search - Component
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cellulase
B: cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4104
Polymers63,8302
Non-polymers5812
Water12,574698
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.500, 78.900, 44.000
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: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 1.6→23 Å / Num. all: 122317 / Num. obs: 53768 / % possible obs: 85.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.08
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.9 % / Num. unique all: 4985 / Rsym value: 0.181 / % possible all: 55.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1TVN

1tvn


Resolution: 1.6→19.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1873081.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2713 5.1 %RANDOM
Rwork0.158 ---
all0.159 122317 --
obs0.159 53650 84.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.5525 Å2 / ksol: 0.40076 e/Å3
Displacement parametersBiso mean: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2---0.84 Å20 Å2
3----0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 38 698 5266
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_mcbond_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.42
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 296 5 %
Rwork0.211 5619 -
obs--57 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4HEPES.PARAMHEPES.TOP
X-RAY DIFFRACTION5CBI.PARAMCBI.TOP

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