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- PDB-1xzb: FUSARIUM SOLANI CUTINASE MUTANT WITH SER 129 REPLACED BY CYS COMP... -

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Basic information

Entry
Database: PDB / ID: 1xzb
TitleFUSARIUM SOLANI CUTINASE MUTANT WITH SER 129 REPLACED BY CYS COMPLEX WITH MERCURY ACETATE
ComponentsCUTINASE
KeywordsHYDROLASE (SERINE ESTERASE) / HYDROLASE / SERINE ESTERASE / 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
MERCURY ACETATE ION / Cutinase 1
Similarity search - Component
Biological speciesNectria haematococca mpVI (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsLonghi, S. / Cambillau, C.
Citation
Journal: To be Published
Title: Core Accessibility of Fusarium Solani Pisi Cutinase Explored by Means of Hg Derivatives of the S129C Mutant
Authors: Longhi, S. / Martinez, C. / Nicolas, A. / Cambillau, C.
#1: Journal: To be Published
Title: Dynamics of Fusarium Solani Cutinase Investigated Through Structural Comparison Among Different Crystal Forms of 34 Variants
Authors: Longhi, S. / Nicolas, A. / Egmond, M. / Verrips, C.T. / Devlieg, J. / Creveld, L. / Martinez, C. / Cambillau, C.
#2: 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.
#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: 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.
#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
DepositionNov 28, 1995Processing site: BNL
Revision 1.0Oct 14, 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 / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CUTINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8863
Polymers22,3671
Non-polymers5192
Water3,891216
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: 22367.082 Da / Num. of mol.: 1 / Mutation: S129C
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH MERCURY ACETATE (MAC) / Source: (gene. exp.) Nectria haematococca mpVI (fungus) / Species: Nectria haematococca / Strain: mpVI / Plasmid: PUC 19 / Production host: Escherichia coli (E. coli)
References: UniProt: P00590, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-MAC / MERCURY ACETATE ION


Mass: 259.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3HgO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE "EPSILON" CONFORMATION OF THE CATALYTIC SERINE IS A TYPICAL FEATURE OF THE ALPHA/BETA HYDROLASE ...THE "EPSILON" CONFORMATION OF THE CATALYTIC SERINE IS A TYPICAL FEATURE OF THE ALPHA/BETA HYDROLASE FAMILY, WHICH CUTINASE BELONGS TO.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37 %

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15907 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
XDSdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.75→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.155 -
obs0.155 15541
Refinement stepCycle: LAST / Resolution: 1.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 10 648 2436
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_deg3.21
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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