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- PDB-6jst: Structure of Geobacillus kaustophilus lactonase, Y99P/D266N doubl... -

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Basic information

Entry
Database: PDB / ID: 6jst
TitleStructure of Geobacillus kaustophilus lactonase, Y99P/D266N double mutant with bound 3-oxo-C8-HSL
ComponentsPhosphotriesteraseAryldialkylphosphatase
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Chem-LAE / HYDROXIDE ION / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.726 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
C: Phosphotriesterase
D: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,02916
Polymers147,2524
Non-polymers77712
Water13,727762
1
A: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1449
Polymers73,6262
Non-polymers5187
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-138 kcal/mol
Surface area22970 Å2
MethodPISA
2
C: Phosphotriesterase
D: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8857
Polymers73,6262
Non-polymers2605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-129 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.991, 51.187, 134.473
Angle α, β, γ (deg.)90.990, 91.330, 96.330
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Phosphotriesterase / Aryldialkylphosphatase


Mass: 36812.883 Da / Num. of mol.: 4 / Mutation: Y99P, 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

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Non-polymers , 5 types, 774 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 17.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO
#5: Chemical ChemComp-LAE / 3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE / N-(3-OXO-OCTANAL-1-YL)-HOMOSERINE LACTONE


Mass: 241.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
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: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→44.917 Å / Num. obs: 142028 / % possible obs: 83.8 % / Redundancy: 1.975 % / CC1/2: 0.995 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.067 / Χ2: 0.98 / Net I/σ(I): 10.73 / Num. measured all: 468131
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
1.73-1.831.9190.2122.836396045780333380.8880.372.8
1.83-1.961.9820.1544.547829843102395090.9330.21891.7
1.96-2.121.9840.1037.226981939880351930.9640.14588.2
2.12-2.321.9840.07510.26145536906309710.9790.10683.9
2.32-2.591.9850.0612.925434133170273750.9830.08482.5
2.59-2.991.9850.04816.14745129408239070.9870.06881.3
2.99-3.661.9830.0419.684032624798203310.9890.05782
3.66-5.161.9870.03321.23304019186166290.9910.04786.7
5.16-44.9171.9840.02721.19194411063098010.9950.03992.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å29.07 Å
Translation3.5 Å29.07 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
Resolution: 1.726→19.986 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.91 / Phase error: 26.49
RfactorNum. reflection% reflection
Rfree0.2639 12924 4.9 %
Rwork0.2187 --
obs0.221 133282 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.32 Å2 / Biso mean: 30.5855 Å2 / Biso min: 3.55 Å2
Refinement stepCycle: final / Resolution: 1.726→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10152 0 28 762 10942
Biso mean--34.84 33.14 -
Num. residues----1292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210439
X-RAY DIFFRACTIONf_angle_d0.9114081
X-RAY DIFFRACTIONf_chiral_restr0.0551517
X-RAY DIFFRACTIONf_plane_restr0.0061863
X-RAY DIFFRACTIONf_dihedral_angle_d4.0126208
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 (%)
1.7257-1.74530.453230.37744674905
1.7453-1.76590.35713150.26966243655869
1.7659-1.78740.29023870.23758573896096
1.7874-1.810.27794400.21828707914796
1.81-1.83380.2733550.22468697905295
1.8338-1.85890.29544790.248550902996
1.8589-1.88540.28464600.24368704916496
1.8854-1.91350.30664750.24058510898596
1.9135-1.94340.27794740.22528651912596
1.9434-1.97530.26454760.22968537901395
1.9753-2.00930.28475430.22288733927697
2.0093-2.04580.26844900.22688575906596
2.0458-2.08510.28284620.23178563902597
2.0851-2.12760.25865510.22228812936396
2.1276-2.17380.29664450.22538532897797
2.1738-2.22430.28794340.22848862929696
2.2243-2.27990.28424050.22778633903897
2.2799-2.34140.26214240.22018849927397
2.3414-2.41020.26094230.21768709913297
2.4102-2.48790.27924210.22178774919597
2.4879-2.57660.26833840.22748856924097
2.5766-2.67950.25215060.23058779928597
2.6795-2.80120.29444550.23448760921598
2.8012-2.94840.26374300.2318815924598
2.9484-3.13250.28254860.2178750923698
3.1325-3.37330.26833500.21318993934398
3.3733-3.71080.23874790.20388789926898
3.7108-4.24330.22374630.19638852931598
4.2433-5.32930.21444250.1898816924199
5.3293-19.98720.26534640.21898806927098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0009-0.0003-0.00150.05720.03150.0266-0.03620.00320.0550.03940.02560.0020.01720.0225-0.02190.02960.0097-0.00940.0572-0.03060.146428.715351.105526.3397
20.0608-0.05790.08910.0579-0.06190.14950.0571-0.06750.0420.01160.03660.0336-0.00510.02890.04310.04-0.02040.04460.1121-0.01870.053915.137136.901629.7649
30.0011-0.0025-0.01020.01490.00410.04450.026-0.03890.06470.00750.00610.0146-0.0266-0.03080.00590.04840.00690.01150.06-0.01890.128920.78444.517125.2225
40.0437-0.02430.03150.0455-0.07850.1455-0.0017-0.03030.0468-0.0328-0.027-0.00040.0691-0.0086-0.00510.02610.0049-0.00290.02090.01640.075527.226936.337620.1251
5-0.0004-0.00060.0010.0038-0.0023-0.0006-0.0342-0.02-0.015-0.03680.0004-0.04420.01240.00200.08570.0050.00830.06530.02040.041329.315835.40815.4405
60.00750.0016-0.00830.00170.00350.0209-0.01210.01930.0222-0.03830.03970.02330.0291-0.00090.00140.05650.00510.00050.04220.00750.105329.789738.310216.3014
70.0073-0.0011-0.00010.0031-0.00070.00230.01490.00540.02790.00890.00370.01110.00320.01060.02190.01290.04560.06280.01930.02640.064837.42737.16810.1846
80.00430.00530.00470.04920.03630.02730.0346-0.07670.0586-0.05360.0132-0.06520.01720.0770.0040.03930.0136-0.00530.0875-0.00350.110743.554836.184723.9292
90.00450.0005-0.00370.0031-0.00440.0060.0137-0.0133-0.03010.0320.04770.01020.0220.02070.00890.1556-0.0123-0.04020.24680.03380.056738.907631.949538.6254
100.077-0.05930.0080.0396-0.00660.0042-0.0577-0.1610.07230.0520.0495-0.0461-0.014-0.0145-0.01880.0915-0.00160.00030.149-0.02090.069532.818139.019837.6306
110.00840.0079-0.00370.0129-0.01090.02630.0250.01940.0066-0.04630.03350.0481-0.0063-0.02220.02770.07920.0026-0.03540.06530.0020.1333-2.532616.10493.6508
120.0182-0.01610.01420.0187-0.01340.00540.03290.0102-0.006-0.0521-0.00670.0503-0.0175-0.00290.0390.09660.0504-0.0625-0.03680.0733-0.000110.021131.23370.2945
130.02670.0032-0.0190.00450.0030.02090.0280.01940.0081-0.06470.00550.0545-0.04370.01850.00560.0699-0.0037-0.01920.05340.0090.07236.515222.67566.7985
140.0041-0.0014-0.00490.00310.00240.00390.0155-0.0412-0.01080.0043-0.0228-0.0312-0.00880.0084-00.0661-0.00370.00850.07040.01950.097613.125117.195824.5812
150.0059-0.01110.01970.0159-0.01330.01920.0304-0.0013-0.0521-0.02250.01820.03890.0329-0.00610.0409-0.01260.1283-0.0576-0.19690.14750.036912.71710.045614.4101
160.0335-0.01780.0070.016-0.00270.01370.04460.004-0.0464-0.0902-0.00920.03780.03790.00150.02190.09010.01-0.01130.05790.00210.101413.74633.73691.395
170.011-0.00650.00830.0151-0.00830.00640.0180.0138-0.0046-0.0081-0.0038-0.01580.0240.0022-0.00470.23920.0655-0.02140.1956-0.07430.153817.62755.9004-9.4654
180.0564-0.0120.03950.02080.00670.03430.05270.0901-0.0358-0.0869-0.0401-0.01540.03850.06570.01220.18670.0244-0.02560.14540.00030.061913.091115.764-8.6722
190.00250.00340.00020.00220.0004-0.00010.0258-0.0078-0.0225-0.0305-0.0030.0187-0.0021-0.00920.00340.14850.0087-0.06370.0759-0.01940.1404-0.76915.5934-3.6863
200.00540.0112-0.00510.0108-0.00530.01360.01060.0292-0.0721-0.04150.0264-0.01930.0488-0.0231-00.2752-0.03250.01850.3376-0.05170.29312.27860.227469.4076
210.011-0.0046-0.00730.00670.0090.0083-0.0390.0469-0.02660.0169-0.0273-0.0096-0.02740.059300.2526-0.02720.01190.3206-0.05510.288616.08899.276979.9529
220.00780.0021-0.00590.0056-0.00170.00760.00520.0032-0.0088-0.0684-0.0020.0178-0.00610.010100.239-0.05220.02360.3972-0.00610.278719.301512.918360.4305
230.0037-0.0028-0.00480.0066-0.00930.0087-0.06090.0320.0428-0.0475-0.04750.09010.02780.006500.24-0.03270.03160.3566-0.07450.25178.24556.55855.4983
240.0034-0.0006-0.0059-0.001-0.0010.00810.0357-0.052-0.031-0.00380.0609-0.04490.0695-0.030500.3282-0.02830.01190.29920.01820.25-5.213115.6678100.2923
250.0084-0.00760.00680.0081-0.0010.00640.00920.0361-0.0185-0.0142-0.03680.0140.01750.0206-00.2522-0.0250.02360.3263-0.07490.2756-6.399818.220495.0385
260.0084-0.0114-0.00390.0183-0.0150.01480.05440.02060.00930.00760.0052-0.0013-0.1259-0.0577-00.25410.00050.02170.3216-0.03590.2633-6.316731.912786.1682
270.00010.0004-0.00060.001-0.00150.00260.0419-0.00920.02410.0181-0.0047-0.0009-0.03590.0076-00.2976-0.0070.01350.2716-0.09380.27964.609535.2078103.8738
280.0030.0031-0.00430.0024-0.00410.0048-0.04290.0271-0.00390.00030.0006-0.0071-0.03890.010200.34870.01360.08510.3091-0.02710.2737-1.667830.56103.3007
290.00350.00350.00220.0104-0.00570.00690.0115-0.0080.00440.0666-0.0582-0.0239-0.02570.0415-00.2165-0.0310.02320.2589-0.0160.18741.523428.0265109.0156
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 88 )A62 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 106 )A89 - 106
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 131 )A107 - 131
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 154 )A132 - 154
7X-RAY DIFFRACTION7chain 'A' and (resid 155 through 171 )A155 - 171
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 228 )A172 - 228
9X-RAY DIFFRACTION9chain 'A' and (resid 229 through 254 )A229 - 254
10X-RAY DIFFRACTION10chain 'A' and (resid 255 through 325 )A255 - 325
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 26 )B3 - 26
12X-RAY DIFFRACTION12chain 'B' and (resid 27 through 61 )B27 - 61
13X-RAY DIFFRACTION13chain 'B' and (resid 62 through 106 )B62 - 106
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 131 )B107 - 131
15X-RAY DIFFRACTION15chain 'B' and (resid 132 through 195 )B132 - 195
16X-RAY DIFFRACTION16chain 'B' and (resid 196 through 235 )B196 - 235
17X-RAY DIFFRACTION17chain 'B' and (resid 236 through 254 )B236 - 254
18X-RAY DIFFRACTION18chain 'B' and (resid 255 through 308 )B255 - 308
19X-RAY DIFFRACTION19chain 'B' and (resid 309 through 325 )B309 - 325
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 88 )C3 - 88
21X-RAY DIFFRACTION21chain 'C' and (resid 89 through 171 )C89 - 171
22X-RAY DIFFRACTION22chain 'C' and (resid 172 through 254 )C172 - 254
23X-RAY DIFFRACTION23chain 'C' and (resid 255 through 325 )C255 - 325
24X-RAY DIFFRACTION24chain 'D' and (resid 3 through 61 )D3 - 61
25X-RAY DIFFRACTION25chain 'D' and (resid 62 through 106 )D62 - 106
26X-RAY DIFFRACTION26chain 'D' and (resid 107 through 222 )D107 - 222
27X-RAY DIFFRACTION27chain 'D' and (resid 223 through 253 )D223 - 253
28X-RAY DIFFRACTION28chain 'D' and (resid 254 through 273 )D254 - 273
29X-RAY DIFFRACTION29chain 'D' and (resid 274 through 325 )D274 - 325

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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