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- PDB-4j35: Molecular Engineering of Organophosphate Hydrolysis Activity from... -

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Basic information

Entry
Database: PDB / ID: 4j35
TitleMolecular Engineering of Organophosphate Hydrolysis Activity from a Weak Promiscuous Lactonase Template
ComponentsPhosphotriesterase, putative
KeywordsHYDROLASE / Organophosphate Hydrolysis Activity / Molecular Engineering
Function / homology
Function and homology information


lactonohydrolase activity / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Phosphotriesterase, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.783 Å
AuthorsSterner, R. / Raushel, F. / Meier, M. / Rajendran, C. / Malisi, C. / Fox, N. / Schlee, S. / Barondeau, D. / Cker, B.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Molecular engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template.
Authors: Meier, M.M. / Rajendran, C. / Malisi, C. / Fox, N.G. / Xu, C. / Schlee, S. / Barondeau, D.P. / Hocker, B. / Sterner, R. / Raushel, F.M.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8043
Polymers34,6861
Non-polymers1182
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphotriesterase, putative
hetero molecules

A: Phosphotriesterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6086
Polymers69,3722
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3800 Å2
ΔGint-78 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.853, 61.853, 204.786
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, putative


Mass: 34686.105 Da / Num. of mol.: 1 / Mutation: Y28L, D71N, Y97F, E101G, E179D, V235L, P274L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9RVU2
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: 0.01 M NiCl2, 0.1 M Tris pH 8.5, 8% PEG MME 2000, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.783→47.464 Å / Num. obs: 44253 / % possible obs: 99.44 % / Observed criterion σ(F): 2.09 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.783→47.464 Å / SU ML: 0.32 / σ(F): 2.09 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 2212 5 %
Rwork0.2013 --
obs0.2026 44253 99.53 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.488 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2605 Å20 Å2-0 Å2
2--0.2605 Å20 Å2
3----0.521 Å2
Refinement stepCycle: LAST / Resolution: 1.783→47.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 2 173 2592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152475
X-RAY DIFFRACTIONf_angle_d1.4773372
X-RAY DIFFRACTIONf_dihedral_angle_d13.509880
X-RAY DIFFRACTIONf_chiral_restr0.078384
X-RAY DIFFRACTIONf_plane_restr0.007447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7828-1.82160.40381280.33712425X-RAY DIFFRACTION93
1.8216-1.86390.32091340.2912559X-RAY DIFFRACTION100
1.8639-1.91060.30171370.25692590X-RAY DIFFRACTION100
1.9106-1.96220.28631360.25872585X-RAY DIFFRACTION100
1.9622-2.020.28841360.22862614X-RAY DIFFRACTION100
2.02-2.08510.23781370.22022594X-RAY DIFFRACTION100
2.0851-2.15970.2531370.22392616X-RAY DIFFRACTION100
2.1597-2.24610.24221370.20732601X-RAY DIFFRACTION100
2.2461-2.34840.24861380.20152628X-RAY DIFFRACTION100
2.3484-2.47220.21031390.20052642X-RAY DIFFRACTION100
2.4722-2.6270.18031380.18642610X-RAY DIFFRACTION100
2.627-2.82990.28271400.21052657X-RAY DIFFRACTION100
2.8299-3.11460.24341380.22362643X-RAY DIFFRACTION100
3.1146-3.56520.27071420.2162695X-RAY DIFFRACTION100
3.5652-4.49120.18681420.17472713X-RAY DIFFRACTION100
4.4912-47.48050.18381530.17672869X-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)
10.2371-0.0372-0.03170.29270.0620.86330.02460.003-0.1557-0.13540.1028-0.09130.14480.0467-0.02340.3934-0.19280.05260.2835-0.05910.2668-9.71713.719216.5841
20.2281-0.17380.35320.64190.28411.4458-0.0504-0.07360.07-0.08860.0518-0.0277-0.21490.0967-0.02240.3962-0.2370.05010.402-0.06170.2585-3.383231.112325.7441
31.02480.17980.10640.7595-0.06850.27840.00360.04030.1924-0.06340.04970.0903-0.12360.0413-0.02440.5412-0.23460.00350.30410.02660.2618-12.403737.201311.49
40.12850.06110.07920.3656-0.08810.27890.01180.0373-0.057-0.16630.12580.1012-0.05840.00730.08440.5332-0.2658-0.01970.36020.05040.3113-20.593923.96526.6264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:91)
2X-RAY DIFFRACTION2chain 'A' and (resseq 92:169)
3X-RAY DIFFRACTION3chain 'A' and (resseq 170:226)
4X-RAY DIFFRACTION4chain 'A' and (resseq 227:323)

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