+Open data
-Basic information
Entry | Database: PDB / ID: 7y0z | |||||||||
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Title | Crystal structure of Pseudomonas aeruginosa PvrA | |||||||||
Components | TetR family transcriptional regulator | |||||||||
Keywords | TRANSCRIPTION / TetR / transcription regulator / DNA binding | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Liang, H. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: Regulatory and structural mechanisms of PvrA-mediated regulation of the PQS quorum-sensing system and PHA biosynthesis in Pseudomonas aeruginosa. Authors: Pan, X. / Liang, H. / Zhao, X. / Zhang, Q. / Chen, L. / Yue, Z. / Yin, L. / Jin, Y. / Bai, F. / Cheng, Z. / Bartlam, M. / Wu, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y0z.cif.gz | 210.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y0z.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 7y0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y0z_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 7y0z_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 7y0z_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 7y0z_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/7y0z ftp://data.pdbj.org/pub/pdb/validation_reports/y0/7y0z | HTTPS FTP |
-Related structure data
Related structure data | 7y0ySC 8hjbC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25071.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) Gene: icaR, acrR5, ALP65_03124, CAZ10_04505, CGU42_03525, DT376_07795, E4V10_02875, E5D53_14345, E5Z62_27065, E5Z63_21855, ECC04_004205, GNQ48_10480, GUL26_15740, I5R60_12040, IPC111_05370, IPC112_ ...Gene: icaR, acrR5, ALP65_03124, CAZ10_04505, CGU42_03525, DT376_07795, E4V10_02875, E5D53_14345, E5Z62_27065, E5Z63_21855, ECC04_004205, GNQ48_10480, GUL26_15740, I5R60_12040, IPC111_05370, IPC112_03820, IPC113_08970, IPC114_03665, IPC115_09445, IPC116_12905, IPC117_01270, IPC118_17205, IPC119_01270, IPC120_08585, IPC121_23995, IPC122_26595, IPC123_13615, IPC124_02210, IPC125_02280, IPC126_02280, IPC127_05520, IPC128_06500, IPC1295_02635, IPC129_03385, IPC1306_00820, IPC1307_00820, IPC1308_01765, IPC1309_01210, IPC130_08705, IPC1310_20400, IPC1311_11055, IPC1312_02745, IPC1313_02755, IPC1314_15055, IPC1315_11085, IPC1316_09415, IPC1317_01215, IPC1318_08785, IPC1319_16990, IPC1320_09215, IPC1321_10825, IPC1322_14910, IPC1323_13890, IPC1324_14335, IPC1325_12685, IPC1326_14415, IPC1327_16075, IPC1328_07000, IPC1329_01215, IPC1330_16860, IPC1331_06735, IPC1332_10900, IPC1333_03260, IPC1334_14490, IPC1335_10585, IPC1336_15040, IPC1337_11350, IPC1338_07490, IPC1339_12735, IPC133_10855, IPC1340_11790, IPC1341_07510, IPC1343_06380, IPC1345_02745, IPC1346_05675, IPC1347_08485, IPC1348_02755, IPC135_13200, IPC137_03780, IPC139_12105, IPC140_07630, IPC141_12315, IPC142_09710, IPC143_09875, IPC144_01055, IPC145_06115, IPC146_01055, IPC1474_02190, IPC1476_02860, IPC1477_06410, IPC1478_01690, IPC1479_15185, IPC147_12070, IPC1480_15440, IPC1481_17805, IPC1482_05515, IPC1485_13825, IPC1486_09235, IPC1487_00765, IPC1488_16575, IPC1489_12290, IPC148_02075, IPC1490_02470, IPC1491_06190, IPC1492_03585, IPC1494_03000, IPC1495_01665, IPC1496_14865, IPC1498_10560, IPC1499_14860, IPC149_01055, IPC1500_06750, IPC1501_01215, IPC1502_04040, IPC1503_01000, IPC1504_01010, IPC1505_13480, IPC1506_19460, IPC1507_05060, IPC1508_10550, IPC1509_14550, IPC150_14460, IPC1510_04225, IPC1511_01525, IPC1512_05030, IPC1513_22270, IPC1514_18185, IPC1515_18905, IPC1516_01320, IPC1517_01215, IPC1518_08030, IPC1519_12340, IPC151_11775, IPC1521_13560, IPC1522_02390, IPC1523_03605, IPC152_09635, IPC153_04910, IPC154_07450, IPC155_07400, IPC156_02990, IPC157_08570, IPC1583_10080, IPC1584_12220, IPC1585_11335, IPC1586_07330, IPC1587_13810, IPC1588_10025, IPC1589_02490, IPC158_07390, IPC1590_14970, IPC1591_08460, IPC1592_11095, IPC1593_06830, IPC1594_02990, IPC1595_05665, IPC1596_09440, IPC1597_09495, IPC1598_01980, IPC1599_03005, IPC159_07400, IPC1600_16790, IPC1601_10780, IPC1602_17245, IPC1603_14770, IPC1604_01745, IPC1605_05455, IPC1606_04825, IPC161_09520, IPC162_09880, IPC163_03825, IPC164_08560, IPC165_03825, IPC166_05525, IPC167_03825, IPC168_20130, IPC169_03825, IPC170_08560, IPC171_16450, IPC172_15260, IPC173_20475, IPC174_05820, IPC175_12970, IPC176_11725, IPC177_13080, IPC178_01215, IPC179_15480, IPC180_10155, IPC181_09045, IPC182_05375, IPC183_01060, IPC184_02640, IPC26_07870, IPC27_04050, IPC29_17535, IPC30_01380, IPC31_02185, IPC32_00905, IPC33_21820, IPC34_13495, IPC35_15445, IPC36_13480, IPC37_01140, IPC38_16530, IPC40_08710, IPC41_10575, IPC43_07930, IPC44_14575, IPC45_08060, IPC46_02025, IPC47_11200, IPC48_15175, IPC49_11615, IPC50_04955, IPC51_01915, IPC54_02210, IPC55_06500, IPC56_01915, IPC574_11290, IPC575_06730, IPC576_12370, IPC577_07725, IPC578_12535, IPC579_11730, IPC57_03340, IPC580_07720, IPC582_13065, IPC584_08355, IPC586_12520, IPC589_07695, IPC58_10915, IPC596_01285, IPC597_08195, IPC598_11110, IPC599_01285, IPC59_19445, IPC600_01285, IPC601_01280, IPC602_01290, IPC603_06120, IPC604_07295, IPC605_06295, IPC606_06290, IPC607_14040, IPC608_02370, IPC609_06890, IPC60_16485, IPC610_02370, IPC611_13025, IPC612_10375, IPC613_14130, IPC614_05225, IPC615_06015, IPC616_11575, IPC618_14040, IPC61_02375, IPC620_19310, IPC621_07445, IPC622_01280, IPC623_18790, IPC624_15950, IPC625_01405, IPC627_01290, IPC629_01405, IPC630_01280, IPC632_13255, IPC633_07865, IPC634_11935, IPC64_06515, IPC65_26010, IPC66_09965, IPC67_22660, IPC68_12530, IPC70_06620, IPC71_07610, IPC72_11155, IPC73_14695, IPC74_10485, IPC75_09820, IPC76_12790, IPC77_07455, IPC78_07465, NCTC13621_02839, PA52Ts2_4326, PAMH19_2113 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072ZS40 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% w/v polyethylene glycol (PEG) 1000, 10% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 21479 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.93 Å2 / Rpim(I) all: 0.048 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Num. unique obs: 1072 / Rpim(I) all: 0.432 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Y0Y Resolution: 2.3→23.49 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.2766 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→23.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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