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- PDB-6jsu: Structure of Geobacillus kaustophilus lactonase, Y99C/D266N doubl... -

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Basic information

Entry
Database: PDB / ID: 6jsu
TitleStructure of Geobacillus kaustophilus lactonase, Y99C/D266N double mutant
ComponentsPhosphotriesterase
KeywordsHYDROLASE / Alpha-Beta Barrel
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / catabolic process / hydrolase activity / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolase
Similarity search - Domain/homology
: / HYDROXIDE ION / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsXue, B. / Yew, W.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (Singapore) Singapore
CitationJournal: Structure / Year: 2020
Title: Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily.
Authors: Go, M.K. / Zhao, L.N. / Xue, B. / Supekar, S. / Robinson, R.C. / Fan, H. / Yew, W.S.
History
DepositionApr 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 17, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 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

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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)73,9148
Polymers73,6382
Non-polymers2776
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-136 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.600, 157.487, 50.618
Angle α, β, γ (deg.)90.000, 117.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphotriesterase


Mass: 36818.910 Da / Num. of mol.: 2 / Mutation: Y99C, D266N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: GK1506 / Plasmid: modified pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 17.00% w/v PEG 20000, 0.10 M TRIS-HCl, pH 8.5, 0.10 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→45.078 Å / Num. obs: 61214 / % possible obs: 98 % / Redundancy: 3.505 % / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 1.159 / Net I/σ(I): 16.01 / Num. measured all: 421538
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.93.4950.2723.496589019932188550.9470.32194.6
1.9-2.043.4070.1565.876243018550183260.980.18698.8
2.04-2.23.5560.0999.646057817313170370.9920.11798.4
2.2-2.413.6320.07214.075732715940157860.9950.08499
2.41-2.693.5150.05518.655026414455142980.9960.06598.9
2.69-3.113.3750.04423.884218312684125000.9970.05298.5
3.11-3.83.6370.03632.313887710790106900.9980.04399.1
3.8-5.353.3970.03235.0827855834982010.9980.03898.2
5.35-45.0783.5330.0336.5316134469145670.9980.03597.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å29.65 Å
Translation3.5 Å29.65 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.7.17phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H9U

4h9u


Resolution: 1.8→19.873 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.25 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.1899 6382 5.32 %
Rwork0.1595 --
obs0.1612 60749 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 31.4311 Å2 / Biso min: 12.16 Å2
Refinement stepCycle: final / Resolution: 1.8→19.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 6 467 5547
Biso mean--20.91 40.06 -
Num. residues----646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125208
X-RAY DIFFRACTIONf_angle_d0.837022
X-RAY DIFFRACTIONf_chiral_restr0.053758
X-RAY DIFFRACTIONf_plane_restr0.006928
X-RAY DIFFRACTIONf_dihedral_angle_d3.5963094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.27292210.23633759398097
1.8205-1.84190.19931650.20623764392998
1.8419-1.86430.29982220.21083763398599
1.8643-1.88790.24981940.20893851404599
1.8879-1.91270.23371740.19143777395198
1.9127-1.93890.24822220.19743766398899
1.9389-1.96660.25312060.20873793399999
1.9666-1.99590.26922310.19483728395998
1.9959-2.0270.28011830.18863803398699
2.027-2.06020.2131710.1873840401198
2.0602-2.09570.23742140.18523746396098
2.0957-2.13380.22621970.17773823402099
2.1338-2.17480.20482360.17573751398799
2.1748-2.21910.21451750.174238534028100
2.2191-2.26730.24421800.17293843402399
2.2673-2.320.2212140.17543788400299
2.32-2.37790.20581940.16813818401299
2.3779-2.44210.23692280.177337894017100
2.4421-2.51380.19532610.16753734399599
2.5138-2.59480.20932510.16963753400499
2.5948-2.68730.22612520.17643724397699
2.6873-2.79460.2072890.17493792408199
2.7946-2.92140.19761830.17193750393399
2.9214-3.07490.19352090.15893793400299
3.0749-3.26680.17942240.152237703994100
3.2668-3.51770.19762140.150338124026100
3.5177-3.86940.16161960.13733847404399
3.8694-4.42390.1292490.12383752400199
4.4239-5.55350.14011880.12573790397898
5.5535-19.87390.14862390.13913763400299
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)
10.0381-0.05380.04420.087-0.06850.2378-0.0017-0.0395-0.03660.10020.1642-0.25820.04650.1040.13940.17960.04710.01890.2101-0.0780.269711.46732.395213.2908
20.19590.0635-0.08860.0234-0.04810.17160.0334-0.0849-0.04970.25210.059-0.04520.20510.14060.09350.45570.0794-0.03140.20310.00570.15196.81269.355231.4862
30.21740.1423-0.1190.0855-0.06180.1208-0.05120.00510.03920.18410.1891-0.12360.05610.20620.06570.1870.0656-0.03470.1964-0.04890.17489.507311.366520.5203
40.0644-0.09040.04530.1955-0.23170.9155-0.1020.1622-0.1258-0.08220.1793-0.1256-0.37110.12580.02820.1928-0.08390.04890.2302-0.06990.197213.368828.451111.4472
50.2536-0.16970.21350.34080.04590.3256-0.15020.0382-0.0523-0.13220.2428-0.2387-0.30930.12950.08120.1205-0.05010.01750.2088-0.04520.16578.244321.00199.6355
60.1624-0.1569-0.01010.50140.09930.0322-0.09650.0175-0.0906-0.32760.06860.1723-0.14040.0114-0.02320.1465-0.0278-0.01510.1806-0.00130.1213-4.031414.23094.813
70.0072-0.02650.01760.2396-0.15660.1012-0.0632-0.011-0.02060.12890.0360.2504-0.0471-0.1441-0.01550.1497-0.04140.05430.2402-0.00340.3362-13.11436.197715.279
80.2947-0.18540.06140.2407-0.00760.1439-0.0456-0.0071-0.14870.34630.11740.38380.0378-0.12620.11480.3099-0.01670.11910.19490.02760.2339-6.91063.671121.1002
90.00130.00190.00130.00310.00060.00490.02080.0013-0.1351-0.00880.05330.03090.16220.0749-00.21810.00630.01650.1968-0.03090.22211.3147-2.86666.6736
100.54360.15970.00570.065-0.07460.2255-0.0180.0405-0.01360.30020.1417-0.18360.12320.03910.14010.33880.0516-0.30.129-0.110.092617.401143.145245.8165
110.0098-0.01430.02730.0359-0.05040.0767-0.1270.03510.19710.01890.1649-0.24960.04580.0193-0.0506-0.2938-0.1045-0.12850.2253-0.18020.361322.927535.445128.0238
120.0320.0374-0.02590.116-0.07020.2826-0.1017-0.0018-0.0240.32450.21-0.22080.0977-0.03630.16010.18670.0325-0.10490.1871-0.05430.199415.157336.404636.5255
130.4316-0.3012-0.21040.21430.17730.3371-0.07860.095-0.09270.383-0.07350.16670.1087-0.102-0.1480.4326-0.04070.13290.1743-0.03070.1662-1.637126.344339.0619
140.01950.099-0.01120.4713-0.07790.01980.0040.0470.0390.28160.030.16860.2069-0.03190.01470.23060.0307-0.02730.16640.00340.13045.282435.110638.0756
150.3147-0.012-0.08520.0102-0.00050.025-0.05820.137-0.10210.3060.02950.25210.0419-0.04480.01550.2896-0.02920.13790.1839-0.00910.291-3.922335.499441.2568
160.34530.13930.29310.10950.09790.3424-0.10030.030.21060.1261-0.06820.3931-0.0517-0.031-0.08530.16370.00890.03190.1504-0.00270.2498-0.921849.849537.2496
170.0179-0.00750.0010.0058-0.00120.004-0.10420.18030.0945-0.2060.05220.077-0.0488-0.0607-0.00010.281-0.0695-0.0220.22090.02060.22568.986957.336327.1476
180.1088-0.05110.06870.2238-0.12710.3922-0.06560.18010.0591-0.09670.1146-0.1271-0.22790.1-0.01440.1795-0.0860.04470.2381-0.03280.217416.259252.448528.1269
190.00120.0012-0.00390.00380.00370.00750.00150.03360.17890.15850.053-0.07940.04530.1052-0.00010.28130.0011-0.03550.1943-0.02670.191613.718155.810645.5947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A3 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 61 )A27 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 106 )A62 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 131 )A107 - 131
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 171 )A132 - 171
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 228 )A172 - 228
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 254 )A229 - 254
8X-RAY DIFFRACTION8chain 'A' and (resid 255 through 308 )A255 - 308
9X-RAY DIFFRACTION9chain 'A' and (resid 309 through 325 )A309 - 325
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 26 )B3 - 26
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 61 )B27 - 61
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 106 )B62 - 106
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 131 )B107 - 131
14X-RAY DIFFRACTION14chain 'B' and (resid 132 through 154 )B132 - 154
15X-RAY DIFFRACTION15chain 'B' and (resid 155 through 171 )B155 - 171
16X-RAY DIFFRACTION16chain 'B' and (resid 172 through 228 )B172 - 228
17X-RAY DIFFRACTION17chain 'B' and (resid 229 through 254 )B229 - 254
18X-RAY DIFFRACTION18chain 'B' and (resid 255 through 308 )B255 - 308
19X-RAY DIFFRACTION19chain 'B' and (resid 309 through 325 )B309 - 325

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