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- PDB-6vli: Crystal structure of transcriptional regulator from bacteriophage 186 -

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Basic information

Entry
Database: PDB / ID: 6vli
TitleCrystal structure of transcriptional regulator from bacteriophage 186
ComponentsRegulatory protein CII
KeywordsGENE REGULATION / DNA binding transcriptional regulator from bacteriophage 186
Function / homologyBacteriophage 186, CII-like / Phage regulatory protein CII (CP76) / DNA binding / ACETATE ION / ACETIC ACID / SUCCINIC ACID / Regulatory protein CII
Function and homology information
Biological speciesEscherichia phage 186 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10002092231 Å
AuthorsTruong, J.Q. / Panjikar, S. / Bruning, J.B. / Shearwin, K.E.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150103009 Australia
Australian Research Council (ARC)DP160101450 Australia
CitationJournal: To Be Published
Title: Crystal structure of a transcriptional regulator from bacteriophage 186
Authors: Truong, J.Q. / Pukala, T. / Panjikar, S. / Bruning, J.B. / Shearwin, K.S.
History
DepositionJan 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein CII
B: Regulatory protein CII
C: Regulatory protein CII
D: Regulatory protein CII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2667
Polymers74,0284
Non-polymers2373
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-151 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.470, 53.510, 106.350
Angle α, β, γ (deg.)90.000, 100.880, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Regulatory protein CII


Mass: 18507.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage 186 (virus) / Gene: CII, CP76 / Production host: Escherichia coli (E. coli) / References: UniProt: P21678
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8 / Details: 8% Tascimate pH 8.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→54.4725150599 Å / Num. obs: 35935 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.5184551105 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.105 / Rrim(I) all: 0.27 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.492 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2958 / CC1/2: 0.528 / Rpim(I) all: 0.627 / Rrim(I) all: 1.622 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXdev_2689refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD model from previous experiments

Resolution: 2.10002092231→54.4725150599 Å / SU ML: 0.260160637355 / Cross valid method: FREE R-VALUE / σ(F): 1.34757867342 / Phase error: 26.6603394611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.260676728826 1995 5.55741266923 %
Rwork0.220865737157 33903 -
obs0.223080930671 35898 99.4046465262 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.7124248631 Å2
Refinement stepCycle: LAST / Resolution: 2.10002092231→54.4725150599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 16 287 4896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002241635843424703
X-RAY DIFFRACTIONf_angle_d0.4829988875946368
X-RAY DIFFRACTIONf_chiral_restr0.0327882603414721
X-RAY DIFFRACTIONf_plane_restr0.00375172934273837
X-RAY DIFFRACTIONf_dihedral_angle_d20.29924776111741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.10002092231-2.15250.3341492243061380.294975855632450X-RAY DIFFRACTION99.5001922338
2.1525-2.21070.3430916954161470.2860236842052391X-RAY DIFFRACTION99.6857816182
2.2107-2.27580.3105076263171300.2697076325232399X-RAY DIFFRACTION99.8026835043
2.2758-2.34930.3339107565041510.261081972162397X-RAY DIFFRACTION99.8041519781
2.3493-2.43320.3062135983681520.26354759952433X-RAY DIFFRACTION99.5379283789
2.4332-2.53060.24746314641250.2465963438352408X-RAY DIFFRACTION99.606763665
2.5306-2.64580.2666585207331640.2408800101022410X-RAY DIFFRACTION99.844840962
2.6458-2.78530.2731682635111300.23508934442430X-RAY DIFFRACTION99.8050682261
2.7853-2.95980.2977743858151430.2400783705752416X-RAY DIFFRACTION99.7272018706
2.9598-3.18830.2305211302441350.221360184482404X-RAY DIFFRACTION99.6467817896
3.1883-3.50910.2602014644911530.212123003552443X-RAY DIFFRACTION99.5017247988
3.5091-4.01670.2549373357681430.1891933585312412X-RAY DIFFRACTION98.9159891599
4.0167-5.06010.1903610922051360.1784271974862432X-RAY DIFFRACTION98.5796545106
5.0601-54.47251505990.2510520731581480.1990584008142478X-RAY DIFFRACTION97.875512486
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)
16.590968064925.934807429793.867202831025.659363725193.958164637163.328035194920.4834887876350.6226910781391.471578352560.261755388991-0.6701974579960.7724303657910.784729349291-0.8545072157620.2079308270450.6641086249350.2967668194790.1828956619130.8864539350160.008623563798070.4390621629258.7287042244-15.987199626899.137049681
23.83559498736-0.881509434531-2.023044081893.54295992729-1.022313389023.02353682633-0.139278413821-0.165422284725-0.8512687474210.04912867165180.04124968703470.3176665704880.001771980875010.02885758460570.1404132011910.194700937878-0.0145729653767-0.004825058487250.0984949644006-0.01965394383150.230950999357-9.59640929207-5.24389571345103.189782199
37.522575855461.217956181170.3955219183186.64653944095-4.745238982644.37684718974-0.10613682132-0.3619831093870.3920662069320.1666561526430.6065161538720.871422870608-0.137110337619-0.83816323902-0.42632974510.2382458771450.09127171031740.01207691862980.281528876505-0.0007993010709250.294134923254-26.66489813297.91087555343105.0218626
46.58836730196-3.15657742511-2.489281994375.75511568163.331347650594.699323722040.02420186841250.153620600551-0.401830614892-0.6379002660240.0661679657771.689121486170.329732082303-1.825620225060.1232164431670.1904192700320.0156850862144-0.02976496700470.4219648016930.03188209314620.385934306593-25.95175191882.6474036565397.1115112937
51.939940540370.07634689916710.09921675057827.25131166156-1.763680954125.23308629966-0.4742825109670.371797131562-0.00362217708986-0.6879308302390.361080026761-0.6616497401280.880691731285-0.9209415404740.2246622133580.28236926188-0.1149427165540.05618152378780.2741556987490.01063136234510.234989137494-19.3234239065-2.8143319426994.9717120514
62.317590007491.840189628141.086647966881.020694906140.457361901122.67794174804-0.09037302544780.0268501786350.3831116703960.116995676736-0.07701563490350.242397102633-0.0492044638793-0.1119864911050.1479327314940.125038303160.02402003188380.01760073390810.075371032310.01633521692310.146415839551-8.594244167897.82383916307106.650020022
77.636207797856.43673573136-0.3094903686745.4821640158-0.1995399980353.628688058150.280055900193-0.4462326432650.467894450230.487613171005-0.2780853450580.325264856759-0.00614397620293-0.316146342020.07314569710850.2111569820040.02486657886840.04685365700360.296337544839-0.0437683467430.189465284959-5.63031956543.33545847766124.915056307
80.972860059927-0.5215576054251.819001673320.275523755265-0.926474303579.80055548896-0.0530122046084-1.661162819220.4175658496040.505266104576-0.05103189980180.6149501774641.25394429983-3.174026146050.04887503774130.901579525139-0.366146831845-0.1447156478311.323734917390.1270411576920.477492283465-15.9702001846-13.9964881696120.893320635
94.357050238134.061469082412.26559043586.386633960252.130453523164.161015236310.088301324967-0.2170484344410.553581501112-0.0446599856535-0.1848087294740.8436650632620.0216508404149-0.2437973099680.1662502443950.1981711769920.04996991658520.02235863062490.19852323036-0.01104157728190.195751119338-4.37221983923.75014863052117.200744072
104.940744082833.407174184840.1314973231834.426333922454.372482751239.71255166470.4640255689050.3609009524820.08977556507750.0815687132604-0.497405013774-0.1471706582080.614411790653-0.4076113070150.4764643901470.3506688482690.172520736907-0.05057378931580.415093629120.09447861441850.369796732441-3.1569008507820.3778803706162.200394333
113.020412321713.4735204133-0.8031488445644.25726620707-1.426890071211.1443967042-0.345278745831-0.0464699852774-1.087361505120.670208143325-0.0576995163164-1.551597592410.8144322172240.0006322392941040.3706557327150.947298153582-0.09282779718460.1657724656220.256566659039-0.05290277782820.625825774062-2.871248573479.51891612742161.375011985
124.591301496150.6438933205545.066373584997.77737808201-0.2661915938526.78771365495-0.2635840757760.01749569514921.236361619570.0461564129237-0.365155755077-0.262539089792-1.053187133250.09728977173860.6143194074540.2415201204560.05685630221720.04744453637030.334001356714-0.01947679340920.336234503652-13.37379679726.90698149416156.913233184
135.57202351833.877698251444.776784019799.245189535140.9373105410945.91562423367-0.516321841130.2348374879360.577729484661-0.4207343277290.5533199924241.35085094689-0.546046215411-0.8421248009150.4362074001920.391026323251-0.00548434658868-0.07978769135280.318237499128-0.007774891904750.415120416983-25.12967570532.51815603882145.997288482
142.59098496497-0.05599951009011.449696845970.07711745543770.7670281671858.676946536190.2249068860540.115889213548-1.02300300803-0.56508208942-0.1981045495751.425492437290.398071533695-1.37760830136-0.187935591560.327387670632-0.0578635677407-0.1595221170570.714248426832-0.05605388100570.783436347185-33.6133634375-9.73600844365143.053906191
153.36864146643-0.5958104673151.486093089711.010626733671.918710405025.84182801283-0.2896905544170.2998521933960.683331499868-0.525291956553-0.2531682413241.66357819229-0.308556352378-2.065919138740.2229068258440.243333764661-0.00229016118909-0.1206519067850.8315845335980.06482051879670.99290180995-36.3181572243-4.91713285055150.697531882
165.92937087219-0.2289909452631.303877267444.365332447121.341726741486.47308294148-0.1162988214890.4841808203840.00755491728938-0.0620496154650.2627838200730.646008112297-0.342070223347-0.6106987082040.03192492439250.164836196155-0.0121136713940.005788339714690.3847175609520.06947503300730.397247165669-27.8668658728-5.41295124684152.34571948
173.91373881129-4.15288900948-2.40069492966.618481365931.718273812182.665002832240.1642817637630.0640530375615-0.120867424551-0.304392872788-0.2210288023930.3745848877710.0357969909528-0.1588426811120.03662507669690.264027874612-0.05009669583190.004910789660070.257087039872-0.004720770692310.134046807553-14.0212426078-5.69347097599147.962299007
182.95005690084-1.282074212491.495662264165.52390694003-6.175792840258.63278172833-0.06785001462560.121423168515-0.455978462979-0.1744203975030.2847019849610.673869914530.483414951096-0.585527533715-0.1438455180230.193548424572-0.02224704319610.04016477641830.331604556213-0.05691848748120.242782213712-6.44358601109-5.08788827654132.747711303
198.13118317934-4.58592578268-1.690733417833.914565628872.832589440393.016757175380.3065287433840.7614124900191.22898178179-1.28398293151.60581425441.238137929130.86066208254-1.66935762661-1.755941802111.114900409610.28994077936-0.002760818557030.7388460530760.2853099043880.738113234288-17.469684923315.1303182547132.091839404
204.35729088052-5.043730168153.624911551397.28065985056-3.953098151283.09963040139-0.0575448805126-0.172990964517-0.4492031578530.07642671310030.2543260628030.7647539627770.12404901775-0.55860952697-0.2711936025970.27956424895-0.01460616240760.02370817588170.347561034665-0.004167474551340.229955441891-9.91519493474-2.37954094328139.948951477
213.172098980461.10164384879-0.3245243882383.16356639559-3.062189573954.46038258501-0.07220481035480.0802424976754-0.263075837526-0.503439120830.1494218905590.5054639211812.246503078270.345291283872-0.364130438360.623429829293-0.05818233316090.02775677805870.3672219891060.01123681936550.37291870654-17.2607580368-17.1091171272147.640838258
226.583214597292.138271907093.419969649233.801963831863.50454805084.385857866860.161349834728-0.240204184175-0.4870601013920.629014998974-0.0927942446885-0.1338689248321.08568081178-0.538168899235-0.2675986057080.476245082050.0394228937380.02852456547030.2520767588970.06028585673760.24095673649-14.3171379648-13.4339051287166.507540758
233.87351167736-2.48229847184-2.590705474146.04821655773-1.895042126464.51671922686-0.221567263535-0.1170101624940.08405054226710.965830692639-0.784890544671-0.64488323393-0.914871349053-0.03101421548830.06263889617060.6013233984160.1637072226350.002054770230510.499248405627-0.1161373950060.181999344029-15.6993011013-1.32165598406175.324752958
246.937469970070.7444685258960.4662333124223.225147527521.390529896335.60773712422-0.01415852962550.135972950407-0.173603042730.5125291471210.1631478475680.6283951745990.288959641983-1.021009230680.06599273841170.3257151702020.06763211545110.1008047979950.2300528890440.003186591203790.223093031484-21.9037624347-5.48463097113167.652466125
251.564364399772.00181004726-1.973701319813.81418206565-3.238350320864.694951200320.147143905001-0.1816245071310.0356188482766-0.0238806943936-0.212261408907-0.0718098446145-0.4290836922270.09246876793180.03530430254090.3418708549820.08404653036530.006587643207980.229364717636-0.04881054524110.200239926434-8.95286850696-2.61179363341153.873684197
266.00023699445-5.85692184813-5.405141112567.342704133255.980915554075.85498989516-0.1531442524230.004698664620270.3441087826450.05642434532980.361254614116-0.232490114503-0.6551878814350.751293356961-0.1675922526710.332340233274-0.0858262716337-0.01786742499690.28774098235-0.01430544709770.2288622883630.978319560254.17524039634135.007145139
270.1127379139161.11072348662-0.855985605711.97957102728-7.849426588836.11764384337-0.219610037044-0.987895582866-0.452074376916-1.73414120398-0.336521146931-0.9326201360982.170752282921.302202831890.3295090010840.901405965070.3736258565450.08160402530241.494344720850.1727089627150.5210416534179.43447210778-14.4713723657132.950899586
285.13044396201-3.82341106044-0.1810123304996.51730732971.472385280776.312224743070.229070906935-0.2026677605060.5041711565220.1016274029440.159238336627-1.2645284719-0.1726007946090.772750669175-0.2424866860420.235047492904-0.0637513413734-0.01460231200580.293932617914-0.01596123521290.302823965836-0.1255144992811.44021816559142.568320691
292.22098827295-1.40991875376-0.5151638426292.928393980471.447735786093.575302336680.08008414705140.2496472772430.143505729028-0.420795448057-0.0206854988371-0.0876152891187-0.2375875447350.119295941829-0.04734333250970.177367449369-0.02641840959330.0423630440530.140433857170.03065792655240.197493398842-4.180890444837.411113425591.4585369079
300.792651764462-0.0464533289389-0.07119749346123.10311361544-1.435672084993.013991978640.00602280653416-0.152109035738-0.1248589037120.0824595702354-0.110573198211-0.2250071102180.2066272510760.202520427040.1119952430740.1677074438660.05552868021410.01661290748840.26492641891-0.01632568846170.3102526767222.71915015419-2.47600649645118.13247541
315.511749452581.779896245431.153762959174.95298576544-0.04394701583344.56317817938-0.4546459374910.0459409374104-0.00690971801607-0.1170783483960.48474971962-0.963761392199-0.5434220639020.7103751631980.03611670319560.2091150926670.0743462046717-0.03796959335010.285839603215-0.01224640749240.394026143237.617205643092.71944779652120.856941033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 111 )
7X-RAY DIFFRACTION7chain 'A' and (resid 112 through 131 )
8X-RAY DIFFRACTION8chain 'A' and (resid 132 through 137 )
9X-RAY DIFFRACTION9chain 'A' and (resid 138 through 165 )
10X-RAY DIFFRACTION10chain 'B' and (resid 13 through 17 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 22 )
12X-RAY DIFFRACTION12chain 'B' and (resid 23 through 30 )
13X-RAY DIFFRACTION13chain 'B' and (resid 31 through 42 )
14X-RAY DIFFRACTION14chain 'B' and (resid 43 through 52 )
15X-RAY DIFFRACTION15chain 'B' and (resid 53 through 62 )
16X-RAY DIFFRACTION16chain 'B' and (resid 63 through 83 )
17X-RAY DIFFRACTION17chain 'B' and (resid 84 through 108 )
18X-RAY DIFFRACTION18chain 'B' and (resid 109 through 131 )
19X-RAY DIFFRACTION19chain 'B' and (resid 132 through 137 )
20X-RAY DIFFRACTION20chain 'B' and (resid 138 through 163 )
21X-RAY DIFFRACTION21chain 'C' and (resid 21 through 30 )
22X-RAY DIFFRACTION22chain 'C' and (resid 31 through 42 )
23X-RAY DIFFRACTION23chain 'C' and (resid 43 through 51 )
24X-RAY DIFFRACTION24chain 'C' and (resid 52 through 83 )
25X-RAY DIFFRACTION25chain 'C' and (resid 84 through 111 )
26X-RAY DIFFRACTION26chain 'C' and (resid 112 through 128 )
27X-RAY DIFFRACTION27chain 'C' and (resid 129 through 138 )
28X-RAY DIFFRACTION28chain 'C' and (resid 139 through 164 )
29X-RAY DIFFRACTION29chain 'D' and (resid 20 through 96 )
30X-RAY DIFFRACTION30chain 'D' and (resid 97 through 130 )
31X-RAY DIFFRACTION31chain 'D' and (resid 131 through 164 )

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