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- PDB-5vej: High resolution crystal structure of a fluoride-inhibited organo-... -

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Basic information

Entry
Database: PDB / ID: 5vej
TitleHigh resolution crystal structure of a fluoride-inhibited organo-phosphate-degrading metallohydrolase
ComponentsPhosphotriesterase
KeywordsHYDROLASE / metallohydrolase / fluoride / inhibited / organo-phosphate-degrading
Function / homology
Function and homology information


catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / FLUORIDE ION / Phosphotriesterase
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.301 Å
AuthorsSelleck, C.
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: High resolution crystal structure of a fluoride-inhibited organophosphate-degrading metallohydrolase.
Authors: Selleck, C. / Guddat, L.W. / Ollis, D.L. / Schenk, G. / Pedroso, M.M.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8436
Polymers35,5891
Non-polymers2555
Water8,521473
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-24 kcal/mol
Surface area12730 Å2
2
A: Phosphotriesterase
hetero molecules

A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,68712
Polymers71,1772
Non-polymers51010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557-x,-x+y,-z+7/31
Buried area4500 Å2
ΔGint-65 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.072, 109.072, 62.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphotriesterase


Mass: 35588.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: opdA / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q93LD7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10 mM MES, pH 6.0, with 0.16 M calcium acetate, 80 mM sodium car-bonate and 14% v/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→47.2 Å / Num. obs: 105162 / % possible obs: 99.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.023 / Net I/σ(I): 15.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D2J

2d2j


Resolution: 1.301→37.744 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.74
RfactorNum. reflection% reflection
Rfree0.1437 2001 1.9 %
Rwork0.1308 --
obs0.1311 105067 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.301→37.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 11 473 2988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072686
X-RAY DIFFRACTIONf_angle_d1.0463661
X-RAY DIFFRACTIONf_dihedral_angle_d13.464991
X-RAY DIFFRACTIONf_chiral_restr0.08413
X-RAY DIFFRACTIONf_plane_restr0.007483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3005-1.3330.19591400.20917148X-RAY DIFFRACTION98
1.333-1.36910.22281400.18797349X-RAY DIFFRACTION100
1.3691-1.40940.19771410.17857311X-RAY DIFFRACTION100
1.4094-1.45480.18361420.1677356X-RAY DIFFRACTION100
1.4548-1.50680.18211420.15247301X-RAY DIFFRACTION100
1.5068-1.56720.171440.14347368X-RAY DIFFRACTION100
1.5672-1.63850.14231420.13637334X-RAY DIFFRACTION100
1.6385-1.72490.14421440.13177355X-RAY DIFFRACTION100
1.7249-1.8330.13641430.13057376X-RAY DIFFRACTION100
1.833-1.97450.14571400.12367388X-RAY DIFFRACTION100
1.9745-2.17320.11931440.11317385X-RAY DIFFRACTION100
2.1732-2.48760.12811410.117411X-RAY DIFFRACTION100
2.4876-3.13380.13991460.1177451X-RAY DIFFRACTION100
3.1338-37.760.13461520.13137533X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0429-0.3978-0.37622.7191.55521.69540.02630.2429-0.2554-0.1891-0.0229-0.0157-0.03150.0255-0.00120.08370.00640.00460.07440.00070.09685.4878-51.598560.7109
22.71630.58350.59731.8406-0.91971.44730.0683-0.1561-0.05240.05-0.0613-0.05460.00970.0306-0.01170.1312-0.02820.00880.143-0.00610.137715.9114-40.427580.9671
33.23613.18131.89783.64741.39951.90150.154-0.1443-0.39810.2038-0.0557-0.26360.14550.0418-0.14820.1086-0.0042-0.00770.12060.02960.15497.0056-53.267978.2672
42.57321.55980.31432.4835-0.27981.21810.04010.0043-0.11680.0668-0.0461-0.11540.03290.11070.00540.08060.01120.01090.0969-0.00430.101210.2201-47.925769.2016
51.40.63070.07351.52-0.02150.6798-0.03810.09420.0437-0.0426-0.0123-0.042-0.04690.07840.05050.0866-0.0057-0.00160.12160.00810.092114.627-36.048461.8771
61.7920.4011-0.15055.97564.46465.1737-0.06170.22180.2193-0.35040.0422-0.0523-0.26750.09570.0420.1233-0.0112-0.01160.16060.0450.126910.7434-29.780854.8628
72.1931-0.0338-0.19560.7834-0.17420.9594-0.0065-0.01660.26880.0350.02540.0725-0.1332-0.0852-0.0290.10080.0132-0.01510.1031-0.00390.1507-4.6653-32.79464.2033
82.4365-0.21311.46571.53220.15143.2291-0.00410.05330.0152-0.08020.02190.1525-0.0352-0.2716-0.0220.10510.0044-0.02870.13810.00820.157-14.3811-41.140261.7525
93.24761.9260.73112.20.87980.47350.1928-0.45130.20830.2094-0.22910.07280.02720.01710.03840.1113-0.0230.01790.1713-0.02170.15410.6508-41.111880.6335
103.4950.1131-0.2530.9706-0.19022.3910.04370.219-0.1234-0.09370.0430.08820.0584-0.2604-0.07490.0912-0.0048-0.01960.0766-0.00470.1332-9.3525-49.462162.2846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 120 )
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 194 )
7X-RAY DIFFRACTION7chain 'A' and (resid 195 through 276 )
8X-RAY DIFFRACTION8chain 'A' and (resid 277 through 298 )
9X-RAY DIFFRACTION9chain 'A' and (resid 299 through 323 )
10X-RAY DIFFRACTION10chain 'A' and (resid 324 through 361 )

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