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- PDB-5w40: Crystal structure of PopP2 F318S in complex with IP6 and AcCoA -

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Basic information

Entry
Database: PDB / ID: 5w40
TitleCrystal structure of PopP2 F318S in complex with IP6 and AcCoA
ComponentsPopP2 protein
KeywordsTRANSCRIPTION / PopP2 / IP6 / AcCoA / Acetyltransferase / YopJ / effector
Function / homologySerine/Threonine acetyltransferase, YopJ / YopJ Serine/Threonine acetyltransferase / acyltransferase activity / COENZYME A / INOSITOL HEXAKISPHOSPHATE / PopP2 protein
Function and homology information
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsZhang, Z.M. / Gao, L. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Plants / Year: 2017
Title: Mechanism of host substrate acetylation by a YopJ family effector.
Authors: Zhang, Z.M. / Ma, K.W. / Gao, L. / Hu, Z. / Schwizer, S. / Ma, W. / Song, J.
History
DepositionJun 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PopP2 protein
B: PopP2 protein
C: PopP2 protein
D: PopP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,43312
Polymers154,7224
Non-polymers5,7108
Water3,783210
1
A: PopP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1083
Polymers38,6811
Non-polymers1,4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PopP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1083
Polymers38,6811
Non-polymers1,4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PopP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1083
Polymers38,6811
Non-polymers1,4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PopP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1083
Polymers38,6811
Non-polymers1,4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.777, 78.645, 79.849
Angle α, β, γ (deg.)103.00, 112.43, 111.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PopP2 protein


Mass: 38680.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: popp, RUN1985_v1_1190012 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4VB05
#2: Chemical
ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 mM imidazole (pH 8.0), 30% (v/v) PEG8000, 200 mM NaCl and 4% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 50251 / % possible obs: 98.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.6 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w3y

5w3y


Resolution: 2.53→39.26 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.05
RfactorNum. reflection% reflection
Rfree0.2354 1923 3.98 %
Rwork0.1878 --
obs0.1897 48342 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.53→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9981 0 296 210 10487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610434
X-RAY DIFFRACTIONf_angle_d1.11714210
X-RAY DIFFRACTIONf_dihedral_angle_d15.8053798
X-RAY DIFFRACTIONf_chiral_restr0.0471624
X-RAY DIFFRACTIONf_plane_restr0.0061844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.59330.31091290.26363310X-RAY DIFFRACTION98
2.5933-2.66340.3071390.24833292X-RAY DIFFRACTION98
2.6634-2.74170.29531300.25083290X-RAY DIFFRACTION98
2.7417-2.83020.29491400.24333281X-RAY DIFFRACTION98
2.8302-2.93130.29951300.23583303X-RAY DIFFRACTION98
2.9313-3.04870.29551480.23573291X-RAY DIFFRACTION99
3.0487-3.18740.27931460.21913315X-RAY DIFFRACTION99
3.1874-3.35530.25561280.20653352X-RAY DIFFRACTION99
3.3553-3.56540.22821410.1953293X-RAY DIFFRACTION99
3.5654-3.84050.22391400.17343357X-RAY DIFFRACTION99
3.8405-4.22650.22161330.1553310X-RAY DIFFRACTION99
4.2265-4.83720.1881420.14743335X-RAY DIFFRACTION99
4.8372-6.09070.22361400.17473340X-RAY DIFFRACTION99
6.0907-39.26470.18781370.16213350X-RAY DIFFRACTION100
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)
14.1871.46910.05682.72340.2691.62750.13630.1792-0.12630.29130.0718-0.4187-0.33520.0481-0.18320.4131-0.0023-0.08390.3881-0.01260.2662-31.0921-22.8891-23.5227
24.21730.43370.15471.99820.47221.84480.1475-1.0370.55270.6944-0.0660.1766-0.5218-0.2889-0.10720.72990.08110.11070.5979-0.09020.394-49.827-17.9345-10.7533
33.15040.04260.38162.66530.40322.72310.0444-0.46350.52610.4419-0.07950.4783-0.7497-0.9966-0.12770.70590.25530.19620.86130.00150.701-64.9346-15.115-14.165
45.77010.3681.84562.15040.13712.5277-0.029-1.09120.70350.75120.26130.545-0.2748-0.6497-0.13510.3380.09110.03280.50340.07830.4007-60.4046-29.2148-25.5545
52.87550.68981.30441.10281.23512.27530.27770.1296-0.2199-0.0747-0.01370.2573-0.0135-0.1241-0.21090.23490.03740.01050.38690.04620.331-53.0036-32.0538-32.2776
64.09982.37231.2462.30580.11762.7736-0.0917-0.22680.09720.0266-0.08890.073-0.26120.10920.08850.27270.0661-0.02210.3308-0.01590.3044-36.6167-24.9725-22.0089
72.2279-2.20121.42413.2244-1.95692.9340.11970.44730.3184-0.336-0.3216-0.35090.12740.39050.16650.3666-0.02830.040.3878-0.01670.3087-57.74390.3635-65.0389
82.7827-0.8085-0.76212.9733-0.51293.17830.0128-0.12860.4420.27590.1388-0.1105-0.5374-0.1846-0.16530.37650.0702-0.02030.2896-0.05450.3294-69.82198.2485-47.8639
94.4081-1.1253-0.86672.68920.2343.36970.0037-0.45090.5240.30920.2408-0.2636-0.5221-0.164-0.17360.3970.046-0.06940.3734-0.08930.3669-66.47885.5978-38.8326
102.3873-1.4346-0.8171.9348-0.21511.4042-0.1211-0.3906-0.07450.27360.21890.0834-0.0177-0.1958-0.07780.34040.0255-0.05220.41620.01740.2449-72.2899-5.191-39.2167
116.58570.76290.7952.7737-0.53712.49340.1773-0.1379-0.2275-0.2553-0.0643-0.1261-0.0646-0.2321-0.05270.30420.0928-0.0250.2530.01850.2979-58.7423-16.4095-45.3428
122.6999-0.62582.06663.0175-2.91254.5372-0.04320.06660.1144-0.31110.143-0.1062-0.0399-0.0548-0.05330.31990.01210.06830.2968-0.04980.2471-60.0143-0.8794-61.2389
134.26262.9453-0.46985.0663-0.52591.8471-0.530.5487-0.1382-0.98520.64020.00710.295-0.3492-0.11390.504-0.0586-0.04520.3854-0.00670.3403-90.6279-43.2891-68.6089
146.2021-1.13680.91794.7294-0.53976.6565-0.02560.11630.9691-0.1735-0.16210.3524-0.4313-0.98590.27220.40450.0245-0.10160.50270.01650.4836-104.0422-33.4329-59.1568
152.9880.6231-0.91741.97540.67643.68310.0381-0.05350.3404-0.0101-0.07270.319-0.2878-0.70720.0830.30730.0575-0.06290.3915-0.04660.3802-98.7656-28.224-46.6567
163.5305-0.2305-1.34790.1343-0.10293.5246-0.064-0.40480.08690.236-0.1161-0.2245-0.0917-0.24570.21670.33820.0283-0.14590.3461-0.07610.4271-83.8018-24.5988-46.5995
174.8670.25211.97942.20420.09183.22030.5421-0.0951-0.3395-0.0401-0.4567-0.35590.23710.1693-0.09330.33760.0254-0.030.31840.07930.3454-74.8508-32.4602-43.9243
183.72430.5353-0.98135.711-2.82456.5710.0220.31040.1182-0.5546-0.1201-0.3515-0.14260.28320.04090.3625-0.06880.01240.2923-0.04020.4636-76.4925-24.0445-62.913
191.76972.3868-0.13086.49770.76892.0143-0.16080.0643-0.2824-0.24810.23960.05540.1342-0.1825-0.09130.3672-0.0579-0.01950.3287-0.01820.2942-93.206-45.415-64.4705
204.5091-1.8845.02283.5332-3.33498.77130.74450.0278-0.2579-0.1977-0.4424-0.15511.07540.7357-0.30450.49860.0006-0.0150.39330.02030.3831-58.3831-69.8729-25.2577
211.368-1.75620.94272.1556-0.79078.59490.07030.0065-0.0784-0.1581-0.28990.33910.3809-0.44380.28980.4827-0.06570.02430.40630.03210.4047-70.4529-63.5406-29.813
222.2767-0.8453-0.14322.4682-0.22471.23620.2531-0.53960.23671.06180.05820.9727-0.0078-0.3923-0.16030.8793-0.11140.45150.7355-0.02060.724-81.235-54.4717-16.9279
234.7213-0.97710.06911.6896-1.31061.8803-0.1598-1.06390.87471.2965-0.15940.5769-0.5249-0.02160.37340.9196-0.03660.24820.552-0.17160.6577-74.9276-42.553-16.6862
242.063-1.4836-0.35741.08120.160.82960.6665-0.25471.38460.8376-0.29850.8266-0.74-0.7603-0.29330.7780.09730.4710.6964-0.15281.0923-85.2742-37.6482-20.6773
251.11.66681.21845.7449-0.73284.5067-0.5257-0.30780.25640.41020.31230.7556-0.3306-0.24510.25960.31430.02570.07270.37490.04640.5912-71.9757-39.6868-34.0012
261.9525-0.25571.56284.8721-2.41332.57770.17770.183-0.02760.3815-0.1770.1250.08850.168-0.07150.34240.0550.08410.32880.00040.291-67.8812-59.6391-30.5837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 143 through 208 )
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 335 )
3X-RAY DIFFRACTION3chain 'A' and (resid 336 through 378 )
4X-RAY DIFFRACTION4chain 'A' and (resid 379 through 401 )
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 427 )
6X-RAY DIFFRACTION6chain 'A' and (resid 428 through 486 )
7X-RAY DIFFRACTION7chain 'B' and (resid 144 through 208 )
8X-RAY DIFFRACTION8chain 'B' and (resid 209 through 286 )
9X-RAY DIFFRACTION9chain 'B' and (resid 287 through 322 )
10X-RAY DIFFRACTION10chain 'B' and (resid 323 through 397 )
11X-RAY DIFFRACTION11chain 'B' and (resid 398 through 440 )
12X-RAY DIFFRACTION12chain 'B' and (resid 441 through 486 )
13X-RAY DIFFRACTION13chain 'C' and (resid 144 through 208 )
14X-RAY DIFFRACTION14chain 'C' and (resid 209 through 238 )
15X-RAY DIFFRACTION15chain 'C' and (resid 239 through 367 )
16X-RAY DIFFRACTION16chain 'C' and (resid 368 through 397 )
17X-RAY DIFFRACTION17chain 'C' and (resid 398 through 412 )
18X-RAY DIFFRACTION18chain 'C' and (resid 413 through 448 )
19X-RAY DIFFRACTION19chain 'C' and (resid 449 through 486 )
20X-RAY DIFFRACTION20chain 'D' and (resid 146 through 178 )
21X-RAY DIFFRACTION21chain 'D' and (resid 179 through 208 )
22X-RAY DIFFRACTION22chain 'D' and (resid 209 through 322 )
23X-RAY DIFFRACTION23chain 'D' and (resid 323 through 351 )
24X-RAY DIFFRACTION24chain 'D' and (resid 352 through 378 )
25X-RAY DIFFRACTION25chain 'D' and (resid 379 through 412 )
26X-RAY DIFFRACTION26chain 'D' and (resid 413 through 487 )

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