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- PDB-1cud: CUTINASE, N172K, R196D MUTANT, MONOCLINIC CRYSTAL FORM WITH THREE... -

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Basic information

Entry
Database: PDB / ID: 1cud
TitleCUTINASE, N172K, R196D MUTANT, MONOCLINIC CRYSTAL FORM WITH THREE MOLECULES PER ASYMMETRIC UNIT
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
Biological speciesNectria haematococca mpVI (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsLonghi, S. / 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: To be Published
Title: Contribution of Cutinase Ser 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: Protein Eng. / Year: 1993
Title: Engineering Cysteine Mutants to Obtain Crystallographic Phases with a Cutinase from Fusarium Solani Pisi
Authors: Martinez, C. / De Geus, P. / Stanssens, P. / Lauwereys, M. / Cambillau, C.
#4: 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 16, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CUTINASE
B: CUTINASE
C: CUTINASE


Theoretical massNumber of molelcules
Total (without water)66,7983
Polymers66,7983
Non-polymers00
Water8,719484
1
C: CUTINASE


Theoretical massNumber of molelcules
Total (without water)22,2661
Polymers22,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CUTINASE


Theoretical massNumber of molelcules
Total (without water)22,2661
Polymers22,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: CUTINASE


Theoretical massNumber of molelcules
Total (without water)22,2661
Polymers22,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.900, 73.300, 71.200
Angle α, β, γ (deg.)90.00, 112.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6966, 0.02763, 0.71693), (0.03338, -0.99942, 0.00608), (0.71668, 0.0197, -0.69712)-14.67947, 38.67043, 32.76411
2given(0.622139, -0.672915, 0.400162), (0.692448, 0.234448, -0.682312), (0.365321, 0.701584, 0.611818)30.58514, 69.71629, -26.07318
3given(0.792539, 0.608716, 0.036698), (0.0374, -0.108583, 0.993384), (0.608673, -0.785923, -0.108823)12.90325, 41.88312, 19.29346

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Components

#1: Protein CUTINASE


Mass: 22265.951 Da / Num. of mol.: 3 / Mutation: N172K, R196E
Source method: isolated from a genetically manipulated source
Details: FORM III CRYSTAL (MONOCLINIC, 3 MOLECULES PER ASYMMETRIC UNIT)
Source: (gene. exp.) Nectria haematococca mpVI (fungus) / Species: Nectria haematococca / Strain: mpVI / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00590, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSER 120: THE "EPSILON" CONFORMATION OF THE CATALYTIC SERINE IS A TYPICAL FEATURE OF THE ALPHA/BETA ...SER 120: 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

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 49 %
Crystal
*PLUS
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

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16170 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.173
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 79908

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Processing

Software
NameVersionClassification
MARXDSdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
MARXDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.7→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.141 -
obs0.141 15469
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5322 0 0 1452 6774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.9
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.151 / Rfactor Rwork: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS

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