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- PDB-3tn4: Crystal structure of GkaP mutant G209D from Geobacillus kaustophi... -

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Basic information

Entry
Database: PDB / ID: 3tn4
TitleCrystal structure of GkaP mutant G209D 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: 1.5 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 19, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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)80,4256
Polymers80,1892
Non-polymers2364
Water16,268903
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-62 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.302, 88.378, 89.684
Angle α, β, γ (deg.)90.00, 99.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 3 - 320 / Label seq-ID: 37 - 354

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

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Components

#1: Protein Phosphotriesterase


Mass: 40094.512 Da / Num. of mol.: 2 / Mutation: G209D
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.: 903 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
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: Dec 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 118387 / % possible obs: 94.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.5-1.554.50.443183.7
1.55-1.625.40.369192.6
1.62-1.695.80.281193.3
1.69-1.785.90.195193.3
1.78-1.895.90.129193.3
1.89-2.046.10.083194.1
2.04-2.246.30.057195.5
2.24-2.566.70.051198.4
2.56-3.237.40.051199.3
3.23-507.50.034198.9

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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: 1.5→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.699 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19829 5946 5 %RANDOM
Rwork0.18069 ---
obs0.18157 112415 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.568 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0.84 Å2
2--0.21 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 4 903 6011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9617068
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15523.73252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24515864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1071538
X-RAY DIFFRACTIONr_chiral_restr0.0820.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214038
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.53212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75825166
X-RAY DIFFRACTIONr_scbond_it1.38732008
X-RAY DIFFRACTIONr_scangle_it2.384.51899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2505 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.310.5
MEDIUM THERMAL0.462
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 370 -
Rwork0.304 7051 -
obs--81.09 %
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)
10.50980.28160.1550.59310.1830.2923-0.0071-0.01490.06040.0165-0.01430.0247-0.00260.01110.02140.0760.0050.0010.0743-0.00840.074517.513-3.154928.4913
20.21220.2450.14440.29480.16910.0988-0.00260.01830.00680.01020.00260.010.00370.010400.0089-0.00330.00140.0223-0.00190.00065.8913-18.229922.404
30.47060.20960.26360.49140.25780.40390.0190.064-0.06540.0279-0.00690.00530.02050.0102-0.01210.07360.0093-0.00750.085-0.02840.0765-4.1331-33.307516.3542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 326
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2A501 - 945
4X-RAY DIFFRACTION2B501 - 958
5X-RAY DIFFRACTION3B3 - 326
6X-RAY DIFFRACTION3B401 - 402

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