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- PDB-3tnb: Crystal structure of GkaP mutant G209D/R230H from Geobacillus kau... -

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Basic information

Entry
Database: PDB / ID: 3tnb
TitleCrystal structure of GkaP mutant G209D/R230H from Geobacillus kaustophilus HTA426
ComponentsPhosphotriesterase
KeywordsHYDROLASE / phosphotriesterase / lactonase
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / hydrolase activity / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsAn, J. / Zhang, Z. / Zhang, Y. / Feng, Y. / Wu, G.
CitationJournal: to be published
Title: Engineering a thermostable lactonase for enhanced phosphotriesterase activity against organophosphate pesticides
Authors: An, J. / Zhang, Z. / Zhang, Y. / Feng, Y. / Wu, G.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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 1.2Dec 6, 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)80,3876
Polymers80,1512
Non-polymers2364
Water12,773709
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-64 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.293, 88.800, 89.314
Angle α, β, γ (deg.)90.000, 98.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 4 - 326 / Label seq-ID: 38 - 360

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein Phosphotriesterase


Mass: 40075.461 Da / Num. of mol.: 2 / Mutation: G209D, R230H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1506 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.51 Å3/Da / Density % sol: 50.95 % / Mosaicity: 0.708 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 13% PEG 8000, 8% ethylene glycol, 2% glycerol, 0.05M sodium hepes pH7.3, vapor diffusion, hanging drop, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 103659 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.056 / Χ2: 1.001 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6670.459103590.9991100
1.66-1.727.10.336103291.002199.9
1.72-1.87.10.244103391.001199.9
1.8-1.97.20.173104081.002199.9
1.9-2.027.20.119103001.001199.9
2.02-2.177.30.083103861199.9
2.17-2.397.30.075103600.998199.8
2.39-2.747.40.077104001.002199.9
2.74-3.457.30.048104190.998199.8
3.45-507.40.03103591.001198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ORW

3orw


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.081 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 5175 5 %RANDOM
Rwork0.1774 ---
obs0.1781 103600 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.46 Å2 / Biso mean: 24.3437 Å2 / Biso min: 10.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-1.05 Å2
2--0.01 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 4 709 5815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225222
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9587070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5655646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90623.858254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52615868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9531536
X-RAY DIFFRACTIONr_chiral_restr0.0740.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214040
X-RAY DIFFRACTIONr_mcbond_it0.5211.53212
X-RAY DIFFRACTIONr_mcangle_it1.00125168
X-RAY DIFFRACTIONr_scbond_it1.40232010
X-RAY DIFFRACTIONr_scangle_it2.4884.51902
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2542 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.330.5
MEDIUM THERMAL0.662
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 399 -
Rwork0.232 7219 -
all-7618 -
obs--99.9 %
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)
10.295-0.31690.13890.4652-0.13170.0887-0.0026-0.00730.046-0.0125-0.013-0.0413-0.0022-0.00960.01560.0206-0.00150.00550.02750.00840.02651.13835.598515.869
20.3143-0.25280.28010.3519-0.21550.26750.0241-0.0435-0.0344-0.0319-0.0008-0.01020.0353-0.0343-0.02330.0289-0.0053-0.00350.03540.02620.030922.8675-24.706827.6934
30.068-0.11730.08170.2195-0.16010.1201-0.0192-0.02070.00680.05150.0205-0.0049-0.0402-0.007-0.00130.045-0.0078-0.01380.05590.02510.054311.4853-9.937821.5443
40.4664-0.40870.1590.514-0.19150.1582-0.0166-0.02940.01730.00720.0116-0.0279-0.0024-0.02390.0050.0088-0.0079-0.00140.01930.00110.00711.4945-7.145722.0421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 326
2X-RAY DIFFRACTION2B3 - 326
3X-RAY DIFFRACTION3A327 - 328
4X-RAY DIFFRACTION3B327 - 328
5X-RAY DIFFRACTION4A329 - 709
6X-RAY DIFFRACTION4B329 - 711

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