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- PDB-3a6z: Crystal structure of Pseudomonas sp. MIS38 lipase (PML) in the op... -

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Basic information

Entry
Database: PDB / ID: 3a6z
TitleCrystal structure of Pseudomonas sp. MIS38 lipase (PML) in the open conformation following dialysis against Ca-free buffer
ComponentsLipase
KeywordsHYDROLASE / Family I.3 lipase / beta-roll / open conformation
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsAngkawidjaja, C. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids
Authors: Angkawidjaja, C. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionSep 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Lipase
C: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,80919
Polymers129,1282
Non-polymers68117
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-110 kcal/mol
Surface area46810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.382, 104.382, 495.175
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Lipase /


Mass: 64563.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (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.: 17 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH8.5, 0.2M ammonium acetate, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Feb 27, 2009 / Details: mirrors
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 87709 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.136 / Rsym value: 0.109 / Net I/σ(I): 13.76
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.1 / Num. unique all: 8579 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BL44XUBSS softwaredata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZVD

2zvd


Resolution: 2.15→48.11 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.263 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.165
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.21965 4397 5 %RANDOM
Rwork0.18244 ---
obs0.18431 83266 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9078 0 17 631 9726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0219266
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.93812593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27651226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30425.346419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.402151351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1381526
X-RAY DIFFRACTIONr_chiral_restr0.1220.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027235
X-RAY DIFFRACTIONr_nbd_refined0.220.24363
X-RAY DIFFRACTIONr_nbtor_refined0.3060.26209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2745
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.510.26
X-RAY DIFFRACTIONr_mcbond_it0.9771.56160
X-RAY DIFFRACTIONr_mcangle_it1.57329505
X-RAY DIFFRACTIONr_scbond_it2.54233583
X-RAY DIFFRACTIONr_scangle_it3.614.53088
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 300 -
Rwork0.216 6036 -
obs--99.22 %

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