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- PDB-1cex: STRUCTURE OF CUTINASE -

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Basic information

Entry
Database: PDB / ID: 1cex
TitleSTRUCTURE OF CUTINASE
ComponentsCUTINASE
KeywordsSERINE ESTERASE / HYDROLASE / 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
Biological speciesNectria haematococca mpVI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å
AuthorsLonghi, S. / Czjzek, M. / Lamzin, V. / Nicolas, A. / Cambillau, C.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Atomic resolution (1.0 A) crystal structure of Fusarium solani cutinase: stereochemical analysis.
Authors: Longhi, S. / Czjzek, M. / Lamzin, V. / Nicolas, A. / Cambillau, C.
#1: Journal: Protein Sci. / Year: 1997
Title: Crystal Structure of Cutinase Covalently Inhibited by a Triglyceride Analogue
Authors: Longhi, S. / Mannesse, M. / Verheij, H.M. / De Haas, G.H. / Egmond, M. / Knoops-Mouthuy, E. / Cambillau, C.
#2: 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.
#3: 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.
#4: 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.
#5: 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
DepositionFeb 18, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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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)22,2791
Polymers22,2791
Non-polymers00
Water4,756264
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: 22278.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nectria haematococca mpVI (fungus) / Species: Nectria haematococca / Strain: mpVI / Plasmid: MIRY / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00590, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CATALYTIC SERINE HAS THE EPSILON CONFORMATION WHICH IS TYPICAL OF ALL THE MEMBERS OF THE ...THE CATALYTIC SERINE HAS THE EPSILON CONFORMATION WHICH IS TYPICAL OF ALL THE MEMBERS OF THE ALPHA/BETA HYDROLASE FAMILY.
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: 1.96 Å3/Da / Density % sol: 37 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Abergel, C., (1990) J. Mol. Biol., 215, 215.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.1 MHEPES1reservoir
315-20 %(w/v)PEG10001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionNum. obs: 86474 / % possible obs: 93.3 % / Redundancy: 2.07 % / Rmerge(I) obs: 0.039
Reflection
*PLUS
Highest resolution: 1 Å / Lowest resolution: 15 Å / Num. measured all: 179064
Reflection shell
*PLUS
Highest resolution: 1 Å / Lowest resolution: 1.01 Å / % possible obs: 99 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SHELXL-93model building
SHELXL-93refinement
SHELXL-93phasing
RefinementResolution: 1→15 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.119 -10 %
all0.094 86474 -
obs--93.3 %
Refinement stepCycle: LAST / Resolution: 1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 0 264 1704
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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