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- PDB-1oxm: STRUCTURE OF CUTINASE -

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Basic information

Entry
Database: PDB / ID: 1oxm
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
Chem-TC4 / Cutinase 1
Similarity search - Component
Biological speciesNectria haematococca mpVI (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLonghi, S. / Cambillau, C.
Citation
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.
#1: 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.
#2: 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.
#3: 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.
#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
DepositionOct 26, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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

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Assembly

Deposited unit
A: CUTINASE
B: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3474
Polymers44,5582
Non-polymers7892
Water3,765209
1
A: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6732
Polymers22,2791
Non-polymers3941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6732
Polymers22,2791
Non-polymers3941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.200, 69.200, 73.300
Angle α, β, γ (deg.)90.00, 93.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.62389, -0.46433, -0.62862), (-0.37925, -0.52343, 0.76301), (-0.68333, 0.71444, 0.15047)
Vector: 65.85388, 78.72206, -12.47664)
DetailsTHERE ARE TWO MOLECULES PER ASYMMETRIC UNIT.

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Components

#1: Protein CUTINASE


Mass: 22278.953 Da / Num. of mol.: 2
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: Chemical ChemComp-TC4 / BUTYL-PHOSPHINIC ACID 2,3-BIS-BUTYLCARBAMOYLOXY-PROPYL ESTER GROUP


Mass: 394.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H35N2O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Compound detailsWT CUTINASE COVALENTLY INHIBITED BY THE TRIGLYCERIDE ANALOGUE TC4 BOUND TO THE CATALYTIC SERINE ...WT CUTINASE COVALENTLY INHIBITED BY THE TRIGLYCERIDE ANALOGUE TC4 BOUND TO THE CATALYTIC SERINE (RESIDUES A 120 AND B 120).
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: 2.11 Å3/Da / Density % sol: 42 %
Crystal growpH: 7 / Details: PEG 6000 IN HEPES 0.1 M PH 7, pH 7.0
Crystal grow
*PLUS
Temperature: 20 ℃ / 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/mlcutinase1drop
20.1 MHEPES1drop
314 %(w/v)PEG60001drop
40.1 MHEPES1reservoir
514 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 291 K
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
ReflectionResolution: 2.3→30 Å / Num. obs: 15569 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.94 % / Rmerge(I) obs: 0.0523 / Net I/σ(I): 25.13
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.1768 / Mean I/σ(I) obs: 6.9 / % possible all: 67.7
Reflection
*PLUS
Num. measured all: 45670

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Processing

Software
NameVersionClassification
MARXDSdata collection
MARSCALEdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE AT 1.6 ANGSTROMS (PDB ENTRY 1CUS)

1cus


Resolution: 2.3→30 Å / Cross valid method: R-FREE / σ(F): 0
Details: THE CATALYTIC SER 120 OF BOTH MOLECULES IN THE ASYMMETRIC UNIT LIES IN AN UNFAVORABLE REGION OF THE RAMACHANDRAN PLOT (EPSILON CONFORMATION) WHICH IS TYPICAL OF ALL MEMBERS OF THE ALPHA/BETA ...Details: THE CATALYTIC SER 120 OF BOTH MOLECULES IN THE ASYMMETRIC UNIT LIES IN AN UNFAVORABLE REGION OF THE RAMACHANDRAN PLOT (EPSILON CONFORMATION) WHICH IS TYPICAL OF ALL MEMBERS OF THE ALPHA/BETA HYDROLASE SUPERFAMILY.
RfactorNum. reflection% reflection
Rfree0.227 777 5 %
Rwork0.163 --
obs0.163 15569 93.8 %
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 52 209 3803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.325
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

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