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- PDB-2z8z: Crystal structure of a platinum-bound S445C mutant of Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 2z8z
TitleCrystal structure of a platinum-bound S445C mutant of Pseudomonas sp. MIS38 lipase
ComponentsLipase
KeywordsHYDROLASE / FAMILY I.3 LIPASE / BETA-ROLL / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


calcium ion binding / extracellular region
Similarity search - Function
: / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAngkawidjaja, C. / You, D.J. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: FEBS Lett. / Year: 2007
Title: Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation
Authors: Angkawidjaja, C. / You, D.J. / Matsumura, H. / Kuwahara, K. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionSep 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 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_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,34715
Polymers64,5801
Non-polymers76714
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.879, 84.404, 87.012
Angle α, β, γ (deg.)90.00, 96.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipase


Mass: 64579.918 Da / Num. of mol.: 1 / Mutation: S445C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: MIS38 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q9RBY1, triacylglycerol lipase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 20000, 0.1M MES, 0.2M calcium acetate, 5mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.071784 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 19, 2007 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071784 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 65946 / Num. obs: 63435 / Observed criterion σ(I): 3.4 / Redundancy: 7.2 % / Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z8X

2z8x


Resolution: 1.8→32.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.37 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.109
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20493 3178 5 %RANDOM
Rwork0.17353 ---
obs0.17512 60247 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.877 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 14 495 5062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214648
X-RAY DIFFRACTIONr_bond_other_d0.0010.024036
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9386317
X-RAY DIFFRACTIONr_angle_other_deg1.04739384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3535615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10725.333210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77715679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3231513
X-RAY DIFFRACTIONr_chiral_restr0.1730.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02955
X-RAY DIFFRACTIONr_nbd_refined0.2330.2947
X-RAY DIFFRACTIONr_nbd_other0.190.23973
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22365
X-RAY DIFFRACTIONr_nbtor_other0.0870.22613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2378
X-RAY DIFFRACTIONr_metal_ion_refined0.110.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.27
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.7930.22
X-RAY DIFFRACTIONr_mcbond_it1.1491.53074
X-RAY DIFFRACTIONr_mcbond_other0.3461.51306
X-RAY DIFFRACTIONr_mcangle_it1.70224766
X-RAY DIFFRACTIONr_scbond_it2.71531800
X-RAY DIFFRACTIONr_scangle_it3.9524.51551
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 204 -
Rwork0.217 3678 -
obs--98.45 %

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