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- PDB-1xzk: FUSARIUM SOLANI CUTINASE COMPLEX WITH DI(ISOPROPYL)PHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1xzk
TitleFUSARIUM SOLANI CUTINASE COMPLEX WITH DI(ISOPROPYL)PHOSPHATE
ComponentsCUTINASE
KeywordsHYDROLASE (SERINE ESTERASE) / HYDROLASE / SERINE ESTERASE / GLYCOPROTEIN
Function / homology
Function and homology information


cutinase / cutinase activity / carbohydrate catabolic process / extracellular region
Similarity search - Function
Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIISOPROPYL PHOSPHONATE / Cutinase 1
Similarity search - Component
Biological speciesNectria haematococca mpVI (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.01 Å
AuthorsMartinez, C. / Cambillau, C.
Citation
Journal: Proteins / Year: 1996
Title: Dynamics of Fusarium solani cutinase investigated through structural comparison among different crystal forms of its variants.
Authors: Longhi, S. / Nicolas, A. / Creveld, L. / Egmond, M. / Verrips, C.T. / de Vlieg, J. / Martinez, C. / Cambillau, C.
#1: Journal: Biochemistry / Year: 1996
Title: Contribution of Cutinase Serine 42 Side Chain to the Stabilization of the Oxyanion Transition State
Authors: Nicolas, A. / Egmond, M. / Verrips, C.T. / De Vlieg, J. / Longhi, S. / Cambillau, C. / Martinez, C.
#2: Journal: Biochemistry / Year: 1994
Title: Cutinase, a Lipolytic Enzyme with a Preformed Oxyanion Hole
Authors: Martinez, C. / Nicolas, A. / Van Tilbeurgh, H. / Egloff, M.P. / Cudrey, C. / Verger, R. / Cambillau, C.
#3: Journal: Nature / Year: 1992
Title: Fusarium Solani Cutinase is a Lipolytic Enzyme with a Catalytic Serine Accessible to Solvent
Authors: Martinez, C. / De Geus, P. / Lauwereys, M. / Matthyssens, G. / Cambillau, C.
History
DepositionNov 28, 1995Processing site: BNL
Revision 1.0Nov 30, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _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: CUTINASE
B: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0344
Polymers44,7022
Non-polymers3322
Water4,738263
1
A: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5172
Polymers22,3511
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5172
Polymers22,3511
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.200, 94.800, 55.000
Angle α, β, γ (deg.)90.00, 101.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.89788, 0.08634, 0.43169), (0.08208, -0.99622, 0.02852), (0.43251, 0.00982, -0.90157)
Vector: -5.0589, 9.3367, 18.7027)

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Components

#1: Protein CUTINASE


Mass: 22351.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH DI(ISOPROPYL)PHOSPHATE / Source: (gene. exp.) Nectria haematococca mpVI (fungus) / Species: Nectria haematococca / Strain: mpVI / Plasmid: PUC 19 / Production host: Escherichia coli (E. coli)
References: UniProt: P00590, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE "EPSILON" CONFORMATION OF THE CATALYTIC SERINE IS A TYPICAL FEATURE OF THE ALPHA/BETA HYDROLASE ...THE "EPSILON" CONFORMATION OF THE CATALYTIC SERINE IS A TYPICAL FEATURE OF THE ALPHA/BETA HYDROLASE FAMILY, WHICH CUTINASE BELONGS TO.
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 43 %
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 8 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-20 %(w/v)PEG60001drop
2100 mMHEPES1drop
35-15 mg/mlcutinase1drop
46 mMn-octyl-beta-D-glucopyranoside1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 22117 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.66 % / Rmerge(I) obs: 0.046
Reflection
*PLUS
Highest resolution: 2.01 Å / Num. measured all: 52036

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.01→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.161 -
obs0.161 21537
Refinement stepCycle: LAST / Resolution: 2.01→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 20 263 3839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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