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- PDB-1e1a: Crystal structure of DFPase from Loligo vulgaris -

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Basic information

Entry
Database: PDB / ID: 1e1a
TitleCrystal structure of DFPase from Loligo vulgaris
ComponentsDIISOPROPYLFLUOROPHOSPHATASE
KeywordsPHOSPHOTRIESTERASE / CALCIUM-BINDING SITE / PHOSPHOTRIESTERASE (PTE) / SELENOMETIONINE / BETA-PROPELLER
Function / homology
Function and homology information


diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding
Similarity search - Function
: / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Diisopropyl-fluorophosphatase
Similarity search - Component
Biological speciesLOLIGO VULGARIS (squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKoepke, J. / Scharff, E.I. / Fritzsch, G. / Luecke, C. / Rueterjans, H.
Citation
Journal: Structure / Year: 2001
Title: Crystal Structure of Diisopropylfluorophosphatase from Loligo Vulgaris
Authors: Scharff, E.I. / Koepke, J. / Fritzsch, G. / Luecke, C. / Rueterjans, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Crystallographic Analysis of Dfpase from Loligo Vulgaris
Authors: Scharff, E.I. / Lucke, C. / Fritzsch, G. / Koepke, J. / Hartleib, J. / Dierl, S. / Ruterjans, H.
History
DepositionApr 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: DIISOPROPYLFLUOROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2013
Polymers35,1211
Non-polymers802
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.900, 81.700, 86.200
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 DIISOPROPYLFLUOROPHOSPHATASE / DFPASE


Mass: 35120.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LOLIGO VULGARIS (squid) / Organ: HEAD GANGLION / Plasmid: PKKHISND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q7SIG4*PLUS, EC: 3.1.8.2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 MES, PH 6.5, 12% PEG6000, 16 DEGREES C, 2 DAYS INCUBATION
Crystal grow
*PLUS
Temperature: 289 K / Method: vapor diffusion, hanging drop
Details: Scharff, E.I., (2001) Acta Crystallogr.,Sect.D, 57, 148.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %(w/v)PEG60001reservoir
20.1 MMES1reservoir
32 mMprotein1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468
DetectorType: MARRESEARCHESARCH / Detector: IMAGE PLATE / Date: Sep 15, 1999 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8468 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 27579 / % possible obs: 95.3 % / Redundancy: 5.26 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.108 / % possible all: 84.4
Reflection
*PLUS
Num. measured all: 145181 / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→100 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 -5 %RANDOM
Rwork0.1763 ---
obs0.1763 27542 95.3 %-
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 42.4 Å2 / ksol: 0.95 e/Å3
Displacement parametersBiso mean: 11 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 2 356 2809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.526
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.6521.5
X-RAY DIFFRACTIONc_mcangle_it1.0672
X-RAY DIFFRACTIONc_scbond_it1.2462
X-RAY DIFFRACTIONc_scangle_it1.9242.5
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2315 -5 %
Rwork0.2269 3132 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18

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