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- PDB-1ggv: CRYSTAL STRUCTURE OF THE C123S MUTANT OF DIENELACTONE HYDROLASE (... -

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Basic information

Entry
Database: PDB / ID: 1ggv
TitleCRYSTAL STRUCTURE OF THE C123S MUTANT OF DIENELACTONE HYDROLASE (DLH) BOUND WITH THE PMS MOIETY OF THE PROTEASE INHIBITOR, PHENYLMETHYLSULFONYL FLUORIDE (PMSF)
ComponentsDIENELACTONE HYDROLASE
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD / DIENELACTONE HYDROLASE / PMSF / PSEUDOMONAS PUTIDA (pAC27)
Function / homology
Function and homology information


carboxymethylenebutenolidase / carboxymethylenebutenolidase activity / catabolic process
Similarity search - Function
: / Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxymethylenebutenolidase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRobinson, A. / Edwards, K.J. / Carr, P.D. / Barton, J.D. / Ewart, G.D. / Ollis, D.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of the C123S mutant of dienelactone hydrolase (DLH) bound with the PMS moiety of the protease inhibitor phenylmethylsulfonyl fluoride (PMSF).
Authors: Robinson, A. / Edwards, K.J. / Carr, P.D. / Barton, J.D. / Ewart, G.D. / Ollis, D.L.
History
DepositionSep 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIENELACTONE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)25,1211
Polymers25,1211
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.080, 51.860, 82.610
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 DIENELACTONE HYDROLASE


Mass: 25121.262 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PAC27 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A114, carboxymethylenebutenolidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: (K+/Na+) phosphate, PMSF, pH 6.3, vapor diffusion/hanging drop, temperature 291.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
23 Mphosphate1drop
31.6-1.8 Mphosphate1reservoir
450-100 mMPMSF1dropin 2-propanol

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 8, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 12109 / % possible obs: 78.7 % / Redundancy: 2.5 %
Reflection shellResolution: 2→2.09 Å / % possible all: 65.2
Reflection
*PLUS
Num. measured all: 30250 / Rmerge(I) obs: 0.117
Reflection shell
*PLUS
% possible obs: 65.2 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
MANUFACTURERSUPPLIED (MSC)data reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIENELACTONE HYDROLASE (WILD-TYPE)

Resolution: 2.5→7 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.151 -
obs0.151 6459
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 10 64 2328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.51
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29

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