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- PDB-3hli: diisopropyl fluorophosphatase (DFPase), active site mutants -

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Basic information

Entry
Database: PDB / ID: 3hli
Titlediisopropyl fluorophosphatase (DFPase), active site mutants
ComponentsDiisopropyl-fluorophosphatase
KeywordsHYDROLASE / phosphotriesterase / beta propeller / calcium binding / Calcium / Metal-binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChen, J.C.-H. / Blum, M.-M.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Reversed enantioselectivity of diisopropyl fluorophosphatase against organophosphorus nerve agents by rational design
Authors: Melzer, M. / Chen, J.C. / Heidenreich, A. / Gab, J. / Koller, M. / Kehe, K. / Blum, M.M.
History
DepositionMay 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: Diisopropyl-fluorophosphatase
B: Diisopropyl-fluorophosphatase
C: Diisopropyl-fluorophosphatase
D: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,15512
Polymers139,8344
Non-polymers3218
Water18,7001038
1
A: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0393
Polymers34,9591
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0393
Polymers34,9591
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0393
Polymers34,9591
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Diisopropyl-fluorophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0393
Polymers34,9591
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.950, 74.490, 118.950
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Diisopropyl-fluorophosphatase / DFPase


Mass: 34958.566 Da / Num. of mol.: 4 / Mutation: E37D, Y144A, R146A, T195M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo vulgaris (squid) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG4, EC: 3.1.8.2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1038 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M KCl, 0.05M HEPES pH 7.5, 35% Pentaerythriol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.007 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2008 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.4→500 Å / Num. all: 226127 / Num. obs: 213535 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 18.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.308 / % possible all: 86.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GVW

2gvw


Resolution: 1.4→24.82 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 10622 -random
Rwork0.205 ---
obs0.205 213535 94.5 %-
all-226127 --
Solvent computationBsol: 35.211 Å2
Displacement parametersBiso max: 45.17 Å2 / Biso mean: 12.107 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.654 Å20 Å20.36 Å2
2--0.91 Å20 Å2
3----0.257 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.4→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9757 0 8 1038 10803
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0044
X-RAY DIFFRACTIONc_angle_deg1.45545
X-RAY DIFFRACTIONc_dihedral_angle_d25.795
X-RAY DIFFRACTIONc_improper_angle_d0.77949
X-RAY DIFFRACTIONc_mcbond_it0.9711.5
X-RAY DIFFRACTIONc_scbond_it1.8542
X-RAY DIFFRACTIONc_mcangle_it1.5052
X-RAY DIFFRACTIONc_scangle_it2.7042.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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