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- PDB-7w2q: Crystal structure of Pseudomonas aeruginosa transcriptional regul... -

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Basic information

Entry
Database: PDB / ID: 7w2q
TitleCrystal structure of Pseudomonas aeruginosa transcriptional regulator PvrA in the narrow conformation
ComponentsProbable transcriptional regulator
KeywordsDNA BINDING PROTEIN / TetR / transcriptinal 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: 1.8 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
B: Probable transcriptional regulator
A: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)50,1442
Polymers50,1442
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-27 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.162, 44.162, 251.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 7 through 204)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSLYSB1 - 198
d_21ens_1LYSLYSA4 - 201

NCS oper: (Code: givenMatrix: (-0.00480135482139, 0.999836894768, 0.0174106534216), (0.999907284046, 0.00457837758451, 0.0128242649264), (0.0127424606763, 0.0174706130225, -0.999766176352)Vector: 27. ...NCS oper: (Code: given
Matrix: (-0.00480135482139, 0.999836894768, 0.0174106534216), (0.999907284046, 0.00457837758451, 0.0128242649264), (0.0127424606763, 0.0174706130225, -0.999766176352)
Vector: 27.9650774844, -28.6936193263, 48.601009649)

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 49.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES,14% PEG 4000

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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: Jul 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→22.08 Å / Num. obs: 44339 / % possible obs: 99.86 % / Redundancy: 12.2 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.82
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 4425 / CC1/2: 0.952

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→22.08 Å / SU ML: 0.1781 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.4236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2142 1995 4.5 %
Rwork0.1838 42317 -
obs0.1852 44312 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 0 197 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01273412
X-RAY DIFFRACTIONf_angle_d2.04844580
X-RAY DIFFRACTIONf_chiral_restr0.0675477
X-RAY DIFFRACTIONf_plane_restr0.0252594
X-RAY DIFFRACTIONf_dihedral_angle_d20.1607452
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.0298831948 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.31861380.25053035X-RAY DIFFRACTION99.65
1.85-1.890.2491460.21653025X-RAY DIFFRACTION99.84
1.89-1.950.25441380.21912990X-RAY DIFFRACTION99.94
1.95-2.010.24071450.2073077X-RAY DIFFRACTION99.97
2.01-2.090.23091410.20322982X-RAY DIFFRACTION100
2.09-2.170.25511480.19772982X-RAY DIFFRACTION100
2.17-2.270.20451430.19313007X-RAY DIFFRACTION100
2.27-2.390.23951450.19293034X-RAY DIFFRACTION100
2.39-2.540.21991430.1973034X-RAY DIFFRACTION100
2.54-2.730.22211490.20223043X-RAY DIFFRACTION100
2.73-3.010.23511390.20643008X-RAY DIFFRACTION100
3.01-3.440.21211400.19933034X-RAY DIFFRACTION99.97
3.44-4.330.19251370.16173037X-RAY DIFFRACTION100
4.33-22.080.18751430.15173029X-RAY DIFFRACTION99.44
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)
15.89511418016-2.37415857738-1.324241468273.14046293064-1.737073705592.61829841197-0.636149095295-0.259898920089-0.1279865898221.512357336250.653607404243-0.397703255172-0.718551071333-0.356688032489-0.1938796792760.728265327315-0.0567501231698-0.03776372274960.783816872712-0.06709340184010.98565562158815.72808051765.5829165631545.861716735
25.08566394441.047274157740.271713007922.819410678020.8835630932131.10456091876-0.200299306801-0.101944274305-0.326365889251-0.08473980866280.17449818545-0.0466916866832-0.009050684630740.1025779346060.007856244566530.270663541154-0.005082197593440.005699534184380.3060550035730.03031288373530.223158069618.35617662948-13.946613593235.7484874699
33.470609623954.08107576808-6.245585529923.34345726843-5.793361158276.686707118990.521617797496-0.3214928492630.6330272407770.489223191362-0.1099275692620.591697686884-0.366848478943-0.0743418021455-0.3983252851730.2626284656210.009170713372890.008978417198520.278643001435-0.02581945233740.4076405841273.60439431916-1.6804950753736.6042448489
41.91884792173-1.867323142370.116410864415.91862172562-1.118201832710.860461694159-0.05762797123210.01197294230950.02485620588180.1008593864580.05440768051320.23861972146-0.1309862483560.0328937659544-0.01126999637570.200691783341-0.0371724758554-0.003239324089020.192919284657-0.0242643192120.19606992282514.4773457093-5.2189864449926.7735495439
55.603633332175.876844472945.297949854336.063318149935.546075421935.01015726280.502175211358-0.536366297665-1.055331621340.981729425042-0.720942639368-0.7278547717831.266202554560.1823054481120.09014368305950.414057664656-0.01136228958490.008871158154080.3462663233460.07214125127290.65628973357723.6498340235-25.946557703330.3814693489
64.02285109201-0.966242223277-0.3071331241590.544323642108-0.6096107488075.370857654870.0030221560583-0.2347797643560.5564363545660.41551581322-0.125734403637-0.0382733784718-0.501388289230.1887752754170.103757370820.192218506136-0.08565956152670.01177864573590.252518112454-0.03977675520.30632471846925.044507851-6.1462787792629.9587768738
76.10104207291-1.08224678886-1.384581024954.182266809751.358653237222.538529699150.08800247485320.95862678640.293130162388-0.868661737888-0.2394448512520.0610215610914-0.397558558071-0.550042747577-0.02835074867990.5961441543570.0476455416035-0.1509722646750.4146112158910.04680353983140.4553385154488.50408368306-25.0071923725-6.12175307841
84.63139484107-0.2905801530730.305042003993.567806545750.2823418992524.610047590850.1259367785430.257599782987-0.186328453577-0.596358490589-0.1617188047720.6635479447280.142760829482-0.512898254110.09529991736820.3776128252210.0153429401948-0.0824784953540.291297438588-0.04164102577030.3272743585047.29782783443-28.713127581.55348586028
90.1681579665440.51353215750.2724655930382.090733680061.177819037790.6502540901760.1279997946892.03031832477-0.191064417508-1.892907476580.277475105476-1.092078276770.1486962593851.78495734418-0.07776208166770.9986974297330.1027095238360.2697123591210.8714271211160.1923226372641.0517544078134.0018100328-11.5934770822.25503480204
109.142609603212.22741329086-0.5247298817655.715623977560.8964301149884.06577289262-0.03474747540160.3558323806730.575105204762-0.01364046906440.0203455768205-0.119270621349-0.3879660866650.2353773525550.171541136790.3331146899280.004508994032510.02142034287160.2202984010810.0231222031060.21727485807722.8978334176-10.463724166911.6081858763
114.483054642061.945618063971.008049783349.44060154421.237418460112.83575485346-0.140354753993-0.0603800671415-0.04681691541230.3739256891040.1015281015430.200155622757-0.31983377182-0.02643227846570.2028007575440.322711468045-0.004184341582-0.002909055597390.249929948921-0.03367855224820.2967188891538.92439150384-21.657657190413.5656069461
126.43783998289-0.185232618223-1.449001269447.232645695370.3797229218298.506923063150.1795571459470.0870378980203-0.1748941588490.4049222300010.05891462142080.3986443002970.906374834153-0.304073690874-0.08846330693430.363774742368-0.0536524653379-0.04676496166030.2126223257680.027386174620.35555976046311.3285801006-36.532161279113.4146693878
135.407345415515.80339761042.794531344157.496642676613.461555496562.39903201597-0.03314299275020.492574943536-0.519627802227-0.2666140260320.31349990628-0.7433981127660.04216811923830.37987077598-0.2704360409770.2286198695780.01025608910460.009752024180090.2364097116710.0007366421621680.31973870126326.7472110546-24.793470963212.1146071963
147.1361076286-1.640312879220.427045377531.75784617297-0.4659627570470.7894159232250.0996885685330.2262812904330.0699357271659-0.0452213389259-0.114370467531-0.04457183294750.02701024680830.1270955242270.08362905250290.230105496719-0.04253456034010.02454962257070.233533443803-0.01595135305540.20804655634323.1725929776-13.857609114121.8944965592
158.230626524641.81024476058-1.354750629245.65302137912-2.207162258943.58037355723-0.2896426466720.7200598812061.10568349674-0.02781670078660.714698453660.97920601635-0.148041671153-0.926876201549-0.2594677384630.259867721144-0.0509253554973-0.003753012931990.3373272726530.0169020293450.5150346817512.46406889814-4.7507701474418.3555454311
162.41499390272-3.027139878491.176448148014.0564930774-1.461321796933.41407096707-0.1585218618890.1637242944570.33340529910.102407219659-0.0202750126637-0.394935383271-0.2858100359250.3803506697330.2343783332790.252021007046-0.05569752045660.03077552963450.232979271594-0.006030000195960.30286722134822.2392044589-3.3328027973818.8364951795
174.790571752570.577852310482-2.566006920134.21297731393-1.100097858365.679908607-0.123051754262-1.13335486484-0.6747036294770.739683232441-0.53750748114-0.5871623569210.355366587860.5318082369240.3897854952490.423181558235-0.048476499937-0.08194734295960.6968599278950.3361658590340.5332410809810.0574472166104-25.300332340851.1814636924
187.302259903537.1871217602-1.285565295779.33294009635-1.152056757683.423004738240.362061125525-0.872748048853-0.1776290149170.47534494766-0.357577952178-0.096435067603-0.155336192535-0.0111520258108-0.03734745236660.258518202574-0.004739075905810.005432518022920.4562483152180.05051208415040.2348144870892.76923734666-13.161135490843.3269689269
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 77 through 84 )AB77 - 8471 - 78
22chain 'A' and (resid 85 through 119 )AB85 - 11979 - 113
33chain 'A' and (resid 120 through 146 )AB120 - 146114 - 140
44chain 'A' and (resid 147 through 174 )AB147 - 174141 - 168
55chain 'A' and (resid 175 through 185 )AB175 - 185169 - 179
66chain 'A' and (resid 186 through 204 )AB186 - 204180 - 198
77chain 'B' and (resid 4 through 29 )BA4 - 291 - 26
88chain 'B' and (resid 30 through 76 )BA30 - 7627 - 73
99chain 'B' and (resid 77 through 84 )BA77 - 8474 - 81
1010chain 'B' and (resid 85 through 97 )BA85 - 9782 - 94
1111chain 'B' and (resid 98 through 112 )BA98 - 11295 - 109
1212chain 'B' and (resid 113 through 119 )BA113 - 119110 - 116
1313chain 'B' and (resid 120 through 146 )BA120 - 146117 - 143
1414chain 'B' and (resid 147 through 174 )BA147 - 174144 - 171
1515chain 'B' and (resid 175 through 185 )BA175 - 185172 - 182
1616chain 'B' and (resid 186 through 204 )BA186 - 204183 - 201
1717chain 'A' and (resid 7 through 56 )AB7 - 561 - 50
1818chain 'A' and (resid 57 through 76 )AB57 - 7651 - 70

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