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- PDB-2cut: CUTINASE, A LIPOLYTIC ENZYME WITH A PREFORMED OXYANION HOLE -

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Basic information

Entry
Database: PDB / ID: 2cut
TitleCUTINASE, A LIPOLYTIC ENZYME WITH A PREFORMED OXYANION HOLE
ComponentsCUTINASE
KeywordsCOMPLEX(SERINE ESTERASE/INHIBITOR) / COMPLEX(SERINE ESTERASE-INHIBITOR) / COMPLEX(SERINE ESTERASE-INHIBITOR) complex
Function / homology
Function and homology information


cutinase activity / cutinase / 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
DIETHYL PHOSPHONATE / Cutinase 1
Similarity search - Component
Biological speciesFusarium solani (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMartinez, C. / Cambillau, C.
CitationJournal: 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.
History
DepositionJun 3, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7222
Polymers20,5841
Non-polymers1381
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.300, 61.100, 72.700
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 CUTINASE /


Mass: 20584.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium solani (fungus)
References: UniProt: P00590, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsIN THE CRYSTAL STRUCTURE THE DIETHYL PARA-NITROPHENYL PHOSPHATE INHIBITOR REACTS WITH SER 120 TO ...IN THE CRYSTAL STRUCTURE THE DIETHYL PARA-NITROPHENYL PHOSPHATE INHIBITOR REACTS WITH SER 120 TO PRODUCE A COVALENT ADDUCT WITH THE LEAVING OF THE PARA-NITROPHENYL GROUP.
Sequence detailsCROSS REFERENCE TO SEQUENCE DATABASE SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME CUTI_FUSSO SEQUENCE ...CROSS REFERENCE TO SEQUENCE DATABASE SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME CUTI_FUSSO SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: CUTI_FUSSO SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ARG 48 ALA 32

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlcutinase-E6001reservoir
215-20 %PEG60001reservoir
30.1 MMES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 12970 / % possible obs: 87.6 % / Redundancy: 3.92 % / Num. measured all: 50967 / Rmerge(I) obs: 0.062

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.181 -
obs0.181 12970
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 8 119 1573
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_deg2.9
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
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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