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- PDB-2iau: Crystal structure of squid ganglion DFPase W244Y mutant -

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Basic information

Entry
Database: PDB / ID: 2iau
TitleCrystal structure of squid ganglion DFPase W244Y mutant
ComponentsDiisopropylfluorophosphatase
KeywordsHYDROLASE / phosphotriesterase / beta-propeller / calcium-binding site
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsScharff, E.I. / Koepke, J. / 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. / Luecke, C. / Fritzsch, G. / Koepke, J. / Hartleib, J. / Dierl, S. / Rueterjans, H.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution
Authors: Koepke, J. / Scharff, E.I. / Luecke, C. / Rueterjans, H. / Fritzsch, G.
#3: Journal: Biochemistry / Year: 2005
Title: Mutational and structural studies of the diisopropylfluorophosphatase from Loligo vulgaris shed new light on the catalytic mechanism of the enzyme
Authors: Katsemi, V. / Luecke, C. / Koepke, J. / Loehr, F. / Maurer, S. / Fritzsch, G. / Rueterjans, H.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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: Diisopropylfluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9183
Polymers34,8371
Non-polymers802
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.901, 81.696, 86.246
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diisopropylfluorophosphatase / E.C.3.1.8.2 / DFPASE


Mass: 34837.367 Da / Num. of mol.: 1 / Mutation: W244Y
Source method: isolated from a genetically manipulated source
Details: Phosphotriesterase / Source: (gene. exp.) Loligo vulgaris (squid) / Organ: head ganglion / Plasmid: PKKHISND / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7SIG4, 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.: 305 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 6000, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 10, 1999
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→90 Å / Num. obs: 50450

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1E1A

1e1a


Resolution: 2→90 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 -random
Rwork0.209 --
obs-50450 -
Refinement stepCycle: LAST / Resolution: 2→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 2 305 2756

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