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- PDB-1ffd: CONTRIBUTION OF CUTINASE SERINE 42 SIDE CHAIN TO THE STABILIZATIO... -

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Basic information

Entry
Database: PDB / ID: 1ffd
TitleCONTRIBUTION OF CUTINASE SERINE 42 SIDE CHAIN TO THE STABILIZATION OF THE OXYANION TRANSITION STATE
ComponentsCUTINASE
KeywordsHYDROLASE (SERINE ESTERASE)
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
Biological speciesNectria haematococca mpVI (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.69 Å
AuthorsCambillau, C. / Martinez, C. / Nicolas, A.
Citation
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.
#1: 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.
#2: 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
DepositionOct 7, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.version
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CUTINASE


Theoretical massNumber of molelcules
Total (without water)22,4371
Polymers22,4371
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.120, 67.360, 37.050
Angle α, β, γ (deg.)90.00, 93.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CUTINASE


Mass: 22437.178 Da / Num. of mol.: 1 / Mutation: N84W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nectria haematococca mpVI (fungus) / Species: Nectria haematococca / Strain: mpVI / Description: ESCHERICHIA COLI CLONING SYSTEM / Plasmid: PUC 19 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00590, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal
*PLUS
Density % sol: 38 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.1 MHEPES1reservoir
310-20 %(w/v)PEG60001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 16, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 17226 / % possible obs: 92.9 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 1.69 Å / Num. measured all: 50283 / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
3.2KW / XDS (IP VERSION)data collection
X-PLORmodel building
X-PLOR3.1refinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 1.69→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.144 -
obs0.144 16350
Displacement parametersBiso mean: 40.4 Å2
Refinement stepCycle: LAST / Resolution: 1.69→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 840 2624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.47
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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