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- PDB-1agy: The 1.15 angstrom refined structure of fusarium solani pisi cutinase -

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Basic information

Entry
Database: PDB / ID: 1agy
TitleThe 1.15 angstrom refined structure of fusarium solani pisi cutinase
ComponentsCUTINASE
KeywordsSERINE ESTERASE / HYDROLASE / GLYCOPROTEIN
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
Biological speciesNectria haematococca mpVI (fungus)
MethodX-RAY DIFFRACTION / RESOLUTION EXTENSION / Resolution: 1.15 Å
AuthorsNicolas, A. / Martinez, C. / 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: 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
DepositionMar 26, 1997Processing site: BNL
Revision 1.0Apr 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CUTINASE


Theoretical massNumber of molelcules
Total (without water)20,8281
Polymers20,8281
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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: 20828.400 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 / Production host: Escherichia coli (E. coli)
References: UniProt: P00590, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREGARDING IDENTITY OF RESIDUE ARG 32, UPON QUESTIONING OF TOMMY CARSTENSEN, AUTHORS SONIA LONGHI ...REGARDING IDENTITY OF RESIDUE ARG 32, UPON QUESTIONING OF TOMMY CARSTENSEN, AUTHORS SONIA LONGHI STATED THE FOLLOWING IN 2009: BASED ON THE AA SEQUENCE, AN ARG IS INDEED SUPPOSED TO OCCUR AT THAT POSITION (SEE BELOW). I DO NOT REMEMBER WHY WE DECIDED TO ASSIGN THE ARG NAME TO THIS RESIDUE IN THE HIGH-RESOLUTION STRUCTURE (GIVEN THAT NO DENSITY COULD BE OBSERVED FOR THE SIDE CHAIN BEYOND THE CB). MOREOVER, IF THERE IS NO ROOM FOR THE ACCOMODATION OF AN ARG SIDE CHAIN, IT IS WELL POSSIBLE THAT AN ALA DOES REALLY OCCUR AND THAT THE ARG COMES FROM A SEQUENCING MISTAKE (OR A SUBSTITUTION DURING THE CLONING PROCEDURE IN THE PLASMID(S) USED FOR RECOMBINANT EXPRESSION). I DO NOT KNOW WHETHER AN ANALYSIS OF THE AA COMPOSITION WAS EVER PERFORMED ON THE RECOMBINANT PROTEIN USED FOR CRYSTALLOGRAPHY. WHEN I ARRIVED IN THE LAB, THE PROTEIN WAS ALREADY AVAILABLE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 15 - 20% PEG 6000, 0.1 M HEPES, 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/mlprotein1drop
20.1 MHEPES1reservoir
315-20 %(w/v)PEG10001reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: NICOLET / Detector: AREA DETECTOR / Date: Jan 1, 1993 / Details: NO
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / Num. obs: 60972 / % possible obs: 95.22 % / Observed criterion σ(I): 0 / Redundancy: 4.09 % / Biso Wilson estimate: 8.43 Å2 / Rmerge(I) obs: 0.01 / Rsym value: 0.01 / Net I/σ(I): 27.46
Reflection shellResolution: 1.15→1.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3.21 / Rsym value: 0.03 / % possible all: 84.2

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Processing

Software
NameClassification
XDSdata scaling
MARSCALEdata reduction
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
MARSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: RESOLUTION EXTENSION
Starting model: CUTINASE STRUCTURE AT 1.6 ANGSTROM RESOLUTION

Resolution: 1.15→20 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 1.15 / Data cutoff low absF: 6 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.197 5860 10 %RANDOM
Rwork0.175 ---
obs0.175 57662 95.3 %-
Displacement parametersBiso mean: 13.54 Å2
Refine analyzeLuzzati sigma a obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 271 1906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg3.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d59.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.566
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
LS refinement shellResolution: 1.15→1.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 623 10 %
Rwork0.4 6378 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARALLH22X.PROTOPH19.PEP
X-RAY DIFFRACTION2TOPALLH22X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg59.96
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.566
LS refinement shell
*PLUS
Rfactor Rfree: 0.4 / Rfactor Rwork: 0.4

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