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- PDB-5w7h: Supercharged arPTE variant R5 -

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Basic information

Entry
Database: PDB / ID: 5w7h
TitleSupercharged arPTE variant R5
ComponentsPhosphotriesterase
KeywordsHYDROLASE / supercharged / organophosphate hydrolase / OP hydrolase / surface modification / OpdA / PTE / phosphotriesterase
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / catabolic process / 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
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsCampbell, E. / Grant, J. / Wang, Y. / Sandhu, M. / Williams, R.J. / Nisbet, D.R. / Perriman, A. / Lupton, D. / Jackson, C.J.
CitationJournal: Adv Biosyst / Year: 2018
Title: Hydrogel-Immobilized Supercharged Proteins
Authors: Campbell, E. / Grant, J. / Wang, Y. / Sandhu, M. / Nisbet, D. / Perriman, A. / Lupton, D. / Jackson, C.J.
History
DepositionJun 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 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
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6096
Polymers74,3472
Non-polymers2624
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-166 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.391, 110.076, 112.277
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 Phosphotriesterase


Mass: 37173.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: opdA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93LD7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.01 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium nitrate, zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→34.88 Å / Num. obs: 188301 / % possible obs: 91.52 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1527 / Net I/σ(I): 15.03
Reflection shellResolution: 2.75→2.848 Å / Redundancy: 13 % / Rmerge(I) obs: 0.5932 / Mean I/σ(I) obs: 4.54 / Num. unique obs: 20742 / CC1/2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D2J

2d2j


Resolution: 2.75→34.877 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 703 4.78 %
Rwork0.2206 --
obs0.2233 14713 90.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→34.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5054 0 4 70 5128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045173
X-RAY DIFFRACTIONf_angle_d0.5276995
X-RAY DIFFRACTIONf_dihedral_angle_d13.5363079
X-RAY DIFFRACTIONf_chiral_restr0.04801
X-RAY DIFFRACTIONf_plane_restr0.004906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.96230.36991300.28913033X-RAY DIFFRACTION100
2.9623-3.26020.30351590.25893036X-RAY DIFFRACTION100
3.2602-3.73150.31811140.26452078X-RAY DIFFRACTION68
3.7315-4.69940.25791270.1932638X-RAY DIFFRACTION85
4.6994-34.87960.22521730.17843225X-RAY DIFFRACTION100
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)
12.3578-0.3861.2191.7236-1.68742.35210.38090.2226-0.2123-0.2223-0.62510.20310.31990.57820.07240.17930.0530.03850.22070.02610.269814.932813.270222.9685
21.34470.66550.42182.0231-0.45710.72570.0908-0.16510.07250.2706-0.08180.1178-0.0307-0.2038-0.02270.2003-0.02470.07350.2917-0.10810.29637.260322.352431.4984
31.59230.53410.00272.45641.41051.4399-0.03480.0669-0.04240.3524-0.1701-0.0324-0.08790.06990.15530.1692-0.0162-0.0040.2994-0.0490.415924.773930.952527.0774
44.23171.23070.99960.9888-0.10413.80380.04240.45130.3028-0.00680.0071-0.0428-0.2986-0.12350.09530.2225-0.0182-0.00990.3220.04560.397217.984130.334410.0261
50.1179-0.4232-0.14951.67030.64260.2691-0.1583-0.30040.1911-0.32630.12730.3651-0.26050.0687-0.0740.4553-0.0336-0.03490.43630.1020.3645-3.064133.187415.2597
62.05970.2602-0.10782.47160.77330.9793-0.03810.2576-0.11410.0879-0.09050.15330.0128-0.13150.15140.1525-0.0007-0.01730.27820.04510.28564.610320.98412.7833
72.3639-0.5170.43952.61740.11492.7098-0.42410.0605-0.52560.33020.09140.3980.6606-0.50550.2790.4841-0.0250.08660.2661-0.0820.36312.908541.720562.6918
80.95620.1601-0.40372.04651.08182.3271-0.168-0.0119-0.26090.46610.0027-0.02540.36240.04050.09090.31160.02270.06240.2052-0.01640.397616.285837.243848.7797
91.451-0.2973-0.02132.19271.1872.2019-0.0749-0.017-0.1113-0.0861-0.04990.51180.0622-0.13570.26150.2218-0.00070.0160.2689-0.08510.34746.162549.766146.4058
102.5625-0.34040.48822.48391.72511.85390.03590.55860.3058-0.1790.2437-0.1588-0.31680.1690.30420.1580.1061-0.04430.1823-0.01280.42610.757260.753452.8451
110.33770.2279-0.19572.10550.60312.8656-0.00610.13880.0924-0.34570.1594-0.4841-0.4350.3019-0.10430.348-0.03170.02140.2319-0.01090.505725.699955.563451.2312
123.1784-0.9769-1.47391.48870.21972.1779-0.255-0.09060.18460.39590.2067-0.1470.33390.18640.05630.42850.0423-0.1070.2223-0.01280.282924.57252.513961.224
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 135 )
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 194 )
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 252 )
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 276 )
6X-RAY DIFFRACTION6chain 'A' and (resid 277 through 362 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 58 )
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 155 )
9X-RAY DIFFRACTION9chain 'B' and (resid 156 through 218 )
10X-RAY DIFFRACTION10chain 'B' and (resid 219 through 252 )
11X-RAY DIFFRACTION11chain 'B' and (resid 253 through 312 )
12X-RAY DIFFRACTION12chain 'B' and (resid 313 through 361 )

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