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- PDB-9igk: Crystal structure of P. syringae phosphinothricin acetyltransfera... -

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Basic information

Entry
Database: PDB / ID: 9igk
TitleCrystal structure of P. syringae phosphinothricin acetyltransferase PSPTO_3321
ComponentsPhosphinothricin N-acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / phosphinothricin
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / CITRIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phosphinothricin N-acetyltransferase
Function and homology information
Biological speciesPseudomonas syringae pv. tomato str. DC3000 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDavies, A.M. / Trentham, D. / Sutton, B.J. / Brown, P.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structure and activity of a phosphinothricin N-acetyltransferase (PSPTO_3321) from Pseudomonas syringae pv. tomato DC3000.
Authors: Davies, A.M. / Trentham, D. / Sutton, B.J. / Brown, P.R.
History
DepositionFeb 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphinothricin N-acetyltransferase
B: Phosphinothricin N-acetyltransferase
C: Phosphinothricin N-acetyltransferase
D: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,45218
Polymers78,5704
Non-polymers1,88214
Water9,638535
1
A: Phosphinothricin N-acetyltransferase
B: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,31210
Polymers39,2852
Non-polymers1,0278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-27 kcal/mol
Surface area15250 Å2
2
C: Phosphinothricin N-acetyltransferase
D: Phosphinothricin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1418
Polymers39,2852
Non-polymers8566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-18 kcal/mol
Surface area15830 Å2
Unit cell
Length a, b, c (Å)105.524, 137.666, 61.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Phosphinothricin N-acetyltransferase


Mass: 19642.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato str. DC3000 (bacteria)
Gene: bar, PSPTO_3321 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q87ZV1

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Non-polymers , 5 types, 549 molecules

#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 and 0.2M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.6→53.39 Å / Num. obs: 119224 / % possible obs: 99.8 % / Redundancy: 9.8 % / Biso Wilson estimate: 22.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Net I/σ(I): 15.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5781 / CC1/2: 0.647 / Rpim(I) all: 49.9 / Rrim(I) all: 123.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→53.39 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 5957 5 %
Rwork0.1867 --
obs0.1878 119130 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→53.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 0 118 535 6022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.976
X-RAY DIFFRACTIONf_dihedral_angle_d16.6242184
X-RAY DIFFRACTIONf_chiral_restr0.062872
X-RAY DIFFRACTIONf_plane_restr0.0111029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.31351910.29343631X-RAY DIFFRACTION97
1.62-1.640.30131960.28833723X-RAY DIFFRACTION99
1.64-1.660.31161960.27463716X-RAY DIFFRACTION100
1.66-1.680.26651980.25083755X-RAY DIFFRACTION100
1.68-1.70.27931970.24713729X-RAY DIFFRACTION100
1.7-1.720.24621970.23753751X-RAY DIFFRACTION100
1.72-1.750.2731960.22213725X-RAY DIFFRACTION100
1.75-1.770.27661970.22763758X-RAY DIFFRACTION100
1.77-1.80.25281950.21983723X-RAY DIFFRACTION100
1.8-1.830.29421980.23173751X-RAY DIFFRACTION100
1.83-1.860.23231970.2233755X-RAY DIFFRACTION100
1.86-1.90.27431980.22093749X-RAY DIFFRACTION100
1.9-1.930.22791980.20743757X-RAY DIFFRACTION100
1.93-1.970.22771970.19373745X-RAY DIFFRACTION100
1.97-2.020.26671990.19563776X-RAY DIFFRACTION100
2.02-2.060.23011980.19363768X-RAY DIFFRACTION100
2.06-2.110.22181990.20023780X-RAY DIFFRACTION100
2.11-2.170.22411960.19863725X-RAY DIFFRACTION100
2.17-2.240.20811980.1853770X-RAY DIFFRACTION100
2.24-2.310.20372000.1843788X-RAY DIFFRACTION100
2.31-2.390.2241990.1813782X-RAY DIFFRACTION100
2.39-2.490.20151990.18393776X-RAY DIFFRACTION100
2.49-2.60.21972000.19223805X-RAY DIFFRACTION100
2.6-2.740.22771990.18613771X-RAY DIFFRACTION100
2.74-2.910.22212000.19343810X-RAY DIFFRACTION100
2.91-3.130.19952020.19623833X-RAY DIFFRACTION100
3.13-3.450.21292010.1923835X-RAY DIFFRACTION100
3.45-3.950.19692040.17533852X-RAY DIFFRACTION100
3.95-4.970.14662030.14263873X-RAY DIFFRACTION100
4.97-53.390.17992090.1683961X-RAY DIFFRACTION97
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)
10.05270.06060.02320.12870.00270.04060.21960.45550.0044-0.1561-0.2710.08940.0733-0.28860.07860.25830.0039-0.03560.45680.04070.1922-0.541521.606628.2918
20.00430.00680.00370.00160.00790.008-0.01680.13380.0608-0.0334-0.2004-0.01570.1376-0.0403-0.00020.35650.0271-0.03850.7024-0.00810.33198.051912.958418.4428
30.05850.00490.0170.01640.02470.02410.07470.1987-0.0860.0026-0.0759-0.06770.2626-0.1097-0.01370.3201-0.0618-0.0360.23550.00240.18325.938412.042834.8951
40.00270.03220.00880.19080.08890.05450.11750.21360.0233-0.012-0.0742-0.05550.1649-0.4547-0.02930.20370.0134-0.0130.36580.06850.19822.576824.2730.8795
50.1005-0.0597-0.15730.1850.10180.23120.10440.2550.3188-0.1227-0.1163-0.16080.0473-0.1150.00870.20510.03660.00020.20870.09030.240414.451725.306931.4728
60.0276-0.01620.00150.00960.0010.00280.03790.19970.0012-0.1082-0.00760.07230.00650.00240.01210.30590.0503-0.03330.32650.20560.419515.564329.089617.7432
70.3533-0.0875-0.00940.1408-0.02380.06130.19560.70750.1303-0.2337-0.17510.1230.0981-0.0754-0.03530.34150.1436-0.01340.43090.20880.270320.609320.908317.7647
80.17360.11680.01120.1003-0.00730.00480.18240.52260.2493-0.1432-0.21140.0220.06910.03680.03220.29430.1085-0.01870.39010.17730.260821.471321.903319.6894
90.009-0.0064-0.00810.0320.02320.01960.0387-0.00910.30650.03690.0418-0.2380.05840.07090.02560.2188-0.0054-0.04790.16740.01780.435825.665628.584743.6702
100.0846-0.03520.00890.0384-0.01780.110.01650.2091-0.05410.0599-0.0533-0.0546-0.00920.0611-0.07030.26720.0535-0.00070.1464-0.01480.273838.8474-3.035134.8935
110.00680.00040.00460.0090.00690.00250.04590.36680.19610.06090.0247-0.1496-0.05520.13210.00030.29430.05270.00110.17610.04450.302233.934910.664940.8176
120.0069-0.00130.00350.0004-0.00720.0069-0.05760.1602-0.01580.12650.00520.0824-0.0602-0.15780.00010.22740.039-0.02950.183-0.01440.325925.7325-2.654234.39
130.08180.0041-0.00710.00970.00770.06590.03650.2032-0.1502-0.0271-0.0495-0.0450.0434-0.2159-0.0030.26380.0567-0.01680.2266-0.01090.262637.5348-2.520829.6119
140.0852-0.0409-0.03780.06940.05180.1140.15510.1621-0.0632-0.1214-0.112-0.0513-0.0723-0.2055-0.00260.27580.1082-0.00920.33830.01260.21331.59746.968225.9475
150.1092-0.04920.02970.13430.03870.10950.3410.6360.1723-0.3964-0.3568-0.122-0.03860.0215-0.00880.34840.1909-0.02540.4634-0.02540.164734.39093.960419.5037
160.0079-0.0019-0.02250.0303-0.00350.08780.09350.07060.1472-0.00160.0557-0.0728-0.09080.1414-0.01290.23040.09740.06160.4470.12560.407942.344916.11226.2994
170.1551-0.17510.00820.2285-0.0910.02670.26730.61390.646-0.1613-0.2258-0.309-0.02320.25390.13250.25780.13380.03110.40210.15580.210132.451617.41725.1482
180.00820.00010.01490.0090.0010.0261-0.03870.0766-0.23690.07330.0831-0.1779-0.01310.0775-00.24130.01790.03530.1749-0.01150.26568.879942.665612.7998
190.127-0.0397-0.01960.0476-0.03180.0344-0.05570.49370.17610.01550.1155-0.0062-0.0854-0.23740.0140.2954-0.00390.03190.35870.08070.218860.867953.2213.1936
200.00060.00510.01170.00050.00840.00990.00810.1413-0.1464-0.07530.11290.13260.0921-0.01380.00010.41940.0184-0.03540.70430.07940.322352.100652.2783-3.7634
210.01240.01210.01110.0301-0.00290.01470.05980.08620.133-0.078-0.00190.0687-0.1991-0.2729-0.00730.27480.12220.03420.24230.03150.203553.083154.888112.9126
220.0255-0.00190.02220.0077-0.00920.0564-0.004-0.01060.0012-0.09620.0981-0.12-0.1671-0.05390.00190.22310.01210.06930.1978-0.00440.255664.638245.51811.0444
230.03670.05130.11540.10240.18130.24990.0795-0.1838-0.1397-0.1341-0.13020.0167-0.3206-0.1916-0.02310.21040.07590.02310.35850.00120.194549.126143.859411.5389
240.0830.02490.09990.03610.03870.10070.19010.1984-0.0544-0.18080.0459-0.0824-0.11490.05530.08530.24350.01850.07040.3702-0.03360.238159.232741.8523.1321
250.07510.08780.1210.12980.12780.20520.129-0.0654-0.42-0.02370.0936-0.2103-0.034-0.16210.05780.1890.022700.26350.02330.272253.905436.211812.1254
260.00650.00870.0010.0109-0.00170.00690.06710.2683-0.1307-0.11340.0099-0.1424-0.1195-0.087-0.00130.2390.05020.05580.4128-0.10580.345253.457734.6509-3.9399
270.0433-0.00030.01330.0149-0.0109-0.01180.01880.6244-0.2235-0.1625-0.0482-0.2404-0.09510.0783-0.00010.27750.0410.02020.41450.00220.288744.826439.5049-3.665
280.22960.04430.10570.22880.04730.06850.19830.0643-0.3728-0.0797-0.0020.0053-0.1052-0.28540.0970.20930.01430.01640.40220.08640.278544.512234.99399.1015
290.0628-0.0226-0.02490.07660.03270.13950.0231-0.0282-0.11210.0487-0.06160.1796-0.111-0.0825-0.06690.25840.0304-0.03940.1260.00660.3117.3350.91813.7637
300.0031-0.00450.01350.0005-0.00410.0123-0.10630.2401-0.2673-0.09520.0682-0.09340.07420.163300.3350.0420.02110.3334-0.04680.464128.846843.052819.6272
310.01-0.01040.00280.0194-0.00040.0073-0.0392-0.04120.0654-0.01290.1377-0.2472-0.10880.19760.01450.2588-0.03360.00530.1869-0.0180.375528.995958.008912.8204
320.0597-0.01770.04890.054-0.01760.1795-0.02250.10430.0091-0.0944-0.0530.1149-0.2558-0.0419-0.00840.23320.0218-0.02290.16750.00440.304918.495751.97218.0445
330.0022-0.0018-0.00010.0040.00930.00970.1066-0.00760.06160.0748-0.0388-0.02110.05370.0335-00.3430.00890.00120.45880.03350.321640.770850.5059-0.8256
340.1339-0.03180.04360.21080.10670.07870.30760.3492-0.1142-0.1359-0.24450.26540.0545-0.0581-0.01440.23830.0399-0.04780.2767-0.01060.284719.993646.69223.1682
350.133-0.0981-0.08460.07430.10340.09020.27160.3414-0.2082-0.0301-0.15670.1975-0.03040.0110.01780.24770.0182-0.04690.2879-0.0310.271226.654238.84212.2351
360.01580.0144-0.01340.0052-0.01160.00990.05040.0327-0.1286-0.0775-0.1239-0.0838-0.0452-0.0687-00.22750.0352-0.0460.3427-0.08590.247830.391835.6463-0.112
370.03260.07160.03320.15510.06590.0281-0.0754-0.1425-0.01030.0046-0.05470.0830.0204-0.1942-0.1634-0.4618-0.043-0.18251.19020.35030.356335.545931.205417.0623
380.0628-0.0232-0.00290.02890.0064-0.00120.10240.4396-0.1577-0.184-0.13980.1141-0.1593-0.10950.00660.30990.082-0.05090.4633-0.01610.184332.116243.2804-6.5841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 138 )
7X-RAY DIFFRACTION7chain 'A' and (resid 139 through 155 )
8X-RAY DIFFRACTION8chain 'A' and (resid 156 through 166 )
9X-RAY DIFFRACTION9chain 'A' and (resid 167 through 179 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 27 )
11X-RAY DIFFRACTION11chain 'B' and (resid 28 through 39 )
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 53 )
13X-RAY DIFFRACTION13chain 'B' and (resid 54 through 74 )
14X-RAY DIFFRACTION14chain 'B' and (resid 75 through 99 )
15X-RAY DIFFRACTION15chain 'B' and (resid 100 through 125 )
16X-RAY DIFFRACTION16chain 'B' and (resid 126 through 138 )
17X-RAY DIFFRACTION17chain 'B' and (resid 139 through 175 )
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 11 )
19X-RAY DIFFRACTION19chain 'C' and (resid 12 through 27 )
20X-RAY DIFFRACTION20chain 'C' and (resid 28 through 39 )
21X-RAY DIFFRACTION21chain 'C' and (resid 40 through 53 )
22X-RAY DIFFRACTION22chain 'C' and (resid 54 through 64 )
23X-RAY DIFFRACTION23chain 'C' and (resid 65 through 83 )
24X-RAY DIFFRACTION24chain 'C' and (resid 84 through 99 )
25X-RAY DIFFRACTION25chain 'C' and (resid 100 through 125 )
26X-RAY DIFFRACTION26chain 'C' and (resid 126 through 138 )
27X-RAY DIFFRACTION27chain 'C' and (resid 139 through 155 )
28X-RAY DIFFRACTION28chain 'C' and (resid 156 through 179 )
29X-RAY DIFFRACTION29chain 'D' and (resid 3 through 28 )
30X-RAY DIFFRACTION30chain 'D' and (resid 29 through 39 )
31X-RAY DIFFRACTION31chain 'D' and (resid 40 through 53 )
32X-RAY DIFFRACTION32chain 'D' and (resid 54 through 74 )
33X-RAY DIFFRACTION33chain 'D' and (resid 75 through 83 )
34X-RAY DIFFRACTION34chain 'D' and (resid 84 through 115 )
35X-RAY DIFFRACTION35chain 'D' and (resid 116 through 138 )
36X-RAY DIFFRACTION36chain 'D' and (resid 139 through 147 )
37X-RAY DIFFRACTION37chain 'D' and (resid 148 through 159 )
38X-RAY DIFFRACTION38chain 'D' and (resid 160 through 175 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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