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- PDB-3tn6: Crystal structure of GkaP mutant R230H from Geobacillus kaustophi... -

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Basic information

Entry
Database: PDB / ID: 3tn6
TitleCrystal structure of GkaP mutant R230H from Geobacillus kaustophilus HTA426
ComponentsPhosphotriesterase
KeywordsHYDROLASE / phosphotriesterase / lactonase / (alpha/beta)8-barrel / amidohydrolase superfamily(AHS)
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)80,2716
Polymers80,0352
Non-polymers2364
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-64 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.147, 88.638, 89.718
Angle α, β, γ (deg.)90.000, 99.060, 90.000
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: VAL / Beg label comp-ID: VAL / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 5 - 320 / Label seq-ID: 39 - 354

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

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Components

#1: Protein Phosphotriesterase


Mass: 40017.422 Da / Num. of mol.: 2 / Mutation: 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.: 689 / 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: 50.98 % / Mosaicity: 0.697 °
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: ADSC QUANTUM 315r / 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: 1.6→50 Å / Num. obs: 103769 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.074 / Χ2: 1.002 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.665.40.449103521.0091100
1.66-1.725.50.337103731.0061100
1.72-1.85.50.246103461.0021100
1.8-1.95.50.178103791.0011100
1.9-2.025.60.128103820.9981100
2.02-2.175.60.094103670.9991100
2.17-2.395.60.079104001.0061100
2.39-2.745.60.077103881.002199.9
2.74-3.455.50.07104541.001199.9
3.45-505.40.057103280.999197.7

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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: 0.955 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.994 / SU ML: 0.063 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22529 5170 5 %RANDOM
Rwork0.20973 ---
obs-103668 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 96.94 Å2 / Biso mean: 24.4957 Å2 / Biso min: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.74 Å2
2--0.35 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 4 689 5749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225174
X-RAY DIFFRACTIONr_angle_refined_deg0.8671.9577001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5945638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81723.81252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92415858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4051536
X-RAY DIFFRACTIONr_chiral_restr0.0560.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213996
X-RAY DIFFRACTIONr_mcbond_it0.1231.53180
X-RAY DIFFRACTIONr_mcangle_it0.23825111
X-RAY DIFFRACTIONr_scbond_it0.35231994
X-RAY DIFFRACTIONr_scangle_it0.6254.51890
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2466 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.20.5
MEDIUM THERMAL0.092
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
Num. reflection% reflection
Rfree351 -
Rwork7228 -
all7579 -
obs-98.93 %
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)
11.37830.42610.29891.3850.39980.9566-0.006-0.08630.1050.062-0.01010.0311-0.05420.00220.01610.02020.0050.0080.0101-0.00180.013917.4227-3.035828.3466
21.00550.3730.42171.31430.37361.13020.01440.1035-0.1388-0.04510.0066-0.00120.12230.0112-0.0210.02880.00730.00220.0274-0.02140.0286-4.2316-33.294816.4384
3-0.3897-0.2224-0.0333-0.54840.23150.34110.03950.014-0.0932-0.0250.0475-0.157-0.0078-0.0069-0.0870.13720.0647-0.1560.0481-0.11740.26278.3884-19.62923.0331
41.01180.63590.26381.01860.25390.41940.0032-0.00070.02280.0112-0.00640.02660.00010.00410.00320.15080.0320.02080.15990.00780.12516.42-16.7423.0145
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 - 690
6X-RAY DIFFRACTION4B329 - 689

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