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- PDB-7w2o: Crystal structure of Pseudomonas aeruginosa transcriptional regul... -

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Basic information

Entry
Database: PDB / ID: 7w2o
TitleCrystal structure of Pseudomonas aeruginosa transcriptional regulator PvrA in the wide conformation
ComponentsProbable transcriptional regulator
KeywordsDNA BINDING PROTEIN / TetR / regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
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
Probable transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.21 Å
AuthorsBao, R. / Zhu, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871615 China
CitationJournal: To be published
Title: Pseudomonas aeruginosa PvrA cooperatively binds to multiple pseudo-palindromic sites to hyper stimulate target gene expression
Authors: Bao, R. / Zhu, Y.B.
History
DepositionNov 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Probable transcriptional regulator
A: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)50,1442
Polymers50,1442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-26 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.098, 84.098, 148.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Probable transcriptional regulator / PvrA


Mass: 25071.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA2957
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HZP1

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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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium sulfate,0.1M sodium cacodylate,30%PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.21→38.03 Å / Num. obs: 9186 / % possible obs: 99.23 % / Redundancy: 18.2 % / Biso Wilson estimate: 76.19 Å2 / CC1/2: 0.993 / Net I/σ(I): 41.11
Reflection shellResolution: 3.21→3.3 Å / Num. unique obs: 864 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.21→38.03 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 34.5081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3136 915 10.01 %
Rwork0.2676 8225 -
obs0.2724 9140 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.18 Å2
Refinement stepCycle: LAST / Resolution: 3.21→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 0 0 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393422
X-RAY DIFFRACTIONf_angle_d0.87074592
X-RAY DIFFRACTIONf_chiral_restr0.0473478
X-RAY DIFFRACTIONf_plane_restr0.0063594
X-RAY DIFFRACTIONf_dihedral_angle_d17.618454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.380.37141250.31931121X-RAY DIFFRACTION97.73
3.38-3.590.36371260.31991145X-RAY DIFFRACTION99.76
3.59-3.870.30391290.29961158X-RAY DIFFRACTION99.46
3.87-4.260.30491300.26611158X-RAY DIFFRACTION99.69
4.26-4.880.27671290.24391172X-RAY DIFFRACTION99.46
4.88-6.140.37821330.2841199X-RAY DIFFRACTION99.85
6.14-38.030.281430.23441272X-RAY DIFFRACTION99.3
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)
12.462056352812.11517203075-1.887771685013.97691819066-0.02208700451552.86660423203-0.3159514174231.08590894468-1.476019686690.881234071090.06745546900880.3168033482411.025787863320.959254548442-0.05715270312080.9594286799180.0697867115420.07328205440480.9371072393140.0404252252041.26738847071-6.1386441851613.223811297620.5623359813
24.410998327430.4327826067461.485693161413.92639731021-2.171758262794.4956241565-0.109222625749-0.6339271149730.1282863584530.4003165554120.2087394040510.117192231740.4833819401320.0997821374472-0.2594402098410.4351537561940.1782136243470.02218924666960.463863456231-0.09503000707580.4383601841655.5559881550930.453114469919.8883921314
36.37832150284-0.915054851585-0.8955969683015.77531559469-2.660856601281.501281347260.9996859337721.859163653420.153921894091-1.589022104640.6752356355510.564280733798-3.11601552013-0.244152510436-0.8815134600162.988424255480.383233603649-0.0891178260221.76170701516-0.1296894535040.912051635932-3.2026609547572.474537561614.7982748857
45.78194096384-3.09830459548-2.083264305257.419829164931.045547995333.148794094970.5918180430940.93819385020.720336391162-1.95445156506-0.4214265639620.43320016037-1.05309198999-0.609199495519-0.2558506637621.165424540580.0146613735094-0.3511100968260.671181633763-0.05982676202190.654074414769-3.4430478368763.707394792311.1542708462
55.00261966353-1.7597062102-0.1278867229764.727692912892.183255982925.19880161348-0.3078493771551.345866425110.302115319991-0.544112859489-0.3626312386950.640636477738-1.34274078787-0.2755236096540.6870622183260.942902069704-0.199834458465-0.3959951181050.41218629588-0.08861210033840.7058565124531.8924296230552.27107196447.03604076277
66.06506215762-0.731556705598-1.800988669022.01726634064-0.5923072150864.89836762429-0.1090626528670.1814941014580.4575630788320.0143733722830.0461244096146-0.201847610455-1.059398968960.0834807843497-0.06628884414750.430823897135-0.316070956392-0.1532407924020.889224421137-0.06165664340030.47405739796811.0756424143.344719629916.1051513928
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 5 through 86 )CA5 - 861 - 82
22chain 'C' and (resid 87 through 204 )CA87 - 20483 - 200
33chain 'A' and (resid 5 through 28 )AB5 - 281 - 24
44chain 'A' and (resid 29 through 86 )AB29 - 8625 - 82
55chain 'A' and (resid 87 through 147 )AB87 - 14783 - 143
66chain 'A' and (resid 148 through 204 )AB148 - 204144 - 200

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