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- PDB-7y0y: Crystal structure of Pseudomonas aeruginosa PvrA (SeMet) -

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Basic information

Entry
Database: PDB / ID: 7y0y
TitleCrystal structure of Pseudomonas aeruginosa PvrA (SeMet)
ComponentsTetR family transcriptional regulator
KeywordsTRANSCRIPTION / TetR / transcription regulator / DNA binding
Function / homology
Function and homology information


Tetracyclin repressor-like, C-terminal domain (WHG) / Tetracyclin repressor-like, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Biofilm operon icaADBC HTH-type negative transcriptional regulator IcaR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsLiang, H. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
Ministry of Science and Technology (MoST, China)2020YFC1807000 China
CitationJournal: 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
DepositionJun 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)50,8002
Polymers50,8002
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-32 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.026, 97.609, 105.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

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Components

#1: Protein TetR family transcriptional regulator / TetR/AcrR family transcriptional regulator / Transcriptional regulator


Mass: 25400.035 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 / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 28197 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.63 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 27
Reflection shellResolution: 2.09→2.14 Å / Num. unique obs: 2708 / Rpim(I) all: 0.209

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→34.88 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.3707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 1974 7 %
Rwork0.2025 26223 -
obs0.2059 28197 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.91 Å2
Refinement stepCycle: LAST / Resolution: 2.09→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 0 284 3479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833266
X-RAY DIFFRACTIONf_angle_d0.91884384
X-RAY DIFFRACTIONf_chiral_restr0.0458458
X-RAY DIFFRACTIONf_plane_restr0.0157565
X-RAY DIFFRACTIONf_dihedral_angle_d8.3253429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.34091220.23811631X-RAY DIFFRACTION86.48
2.14-2.20.27681390.23081869X-RAY DIFFRACTION98.48
2.2-2.260.36161230.27861717X-RAY DIFFRACTION91.27
2.26-2.340.28611390.22591814X-RAY DIFFRACTION95.27
2.34-2.420.28041430.20721870X-RAY DIFFRACTION99.31
2.42-2.520.26271410.21131905X-RAY DIFFRACTION99.66
2.52-2.630.24791460.21691880X-RAY DIFFRACTION99.85
2.63-2.770.27071330.22271902X-RAY DIFFRACTION99.46
2.77-2.940.29011480.2311905X-RAY DIFFRACTION99.9
2.94-3.170.24161550.20341895X-RAY DIFFRACTION99.9
3.17-3.490.25261410.20211924X-RAY DIFFRACTION99.95
3.49-3.990.20261440.1811926X-RAY DIFFRACTION99.86
3.99-5.030.23011520.17611948X-RAY DIFFRACTION100
5.03-34.880.24091480.19382037X-RAY DIFFRACTION99.91
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)
12.03266549973-0.894270883278-0.8333962240212.331063217170.7764689506092.086085805350.009220413192960.46475959778-0.122615004524-0.317528511262-0.1280718992020.2367321323920.153388073318-0.2021199235710.06568254329690.247461426684-0.0450130724861-0.04532672487720.2902632968150.01403823047470.16707327900936.35361675911.1135819411214.2061494007
24.197682577071.64680057461-0.5142980276342.55282107999-0.4984007252891.353823005950.162663215076-0.3825197232820.1101257332840.357027173456-0.1431903883590.00142430350257-0.03170577458010.0459965805445-0.03123342601520.2257140004530.01365655229190.001775993835270.244487434538-0.05012903337060.16279887986214.14408990160.84865384909435.6979901578
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 5 through 202)AA5 - 2021 - 193
22(chain 'B' and resid 8 through 202)BB8 - 2021 - 189

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