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- PDB-8c3k: PaaR2 N-terminal domin in complex with nanobody 33 -

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Basic information

Entry
Database: PDB / ID: 8c3k
TitlePaaR2 N-terminal domin in complex with nanobody 33
Components
  • Nanobody 33
  • Phage repressor protein CI
KeywordsDNA BINDING PROTEIN / CI repressor / DNA binding / HTH motif / Helix-turn-helix / nanobody complex / nanobody
Function / homologyPhage repressor protein CI
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74972472153 Å
AuthorsLoris, R. / Prolic-Kalinsek, M.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0226.17N Belgium
CitationJournal: To be published
Title: PaaR2, the CI equivalent in Escherichia coli O157:H7 cryptic prophage CP-933P
Authors: Prolik-Kalinsek, M. / Volkov, A. / Loris, R.
History
DepositionDec 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage repressor protein CI
B: Nanobody 33


Theoretical massNumber of molelcules
Total (without water)21,6062
Polymers21,6062
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-3 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.143, 67.143, 69.707
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Phage repressor protein CI


Mass: 8784.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs_2279 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XAD6
#2: Antibody Nanobody 33


Mass: 12821.132 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.02 M sodium/potassium phosphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.74972472153→44.7 Å / Num. obs: 18742 / % possible obs: 99.8 % / Redundancy: 19.8 % / Biso Wilson estimate: 33.9988668461 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.065 / Net I/σ(I): 23.98
Reflection shellResolution: 1.75→1.86 Å / Rmerge(I) obs: 3.543 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 2961 / CC1/2: 0.589 / Rrim(I) all: 3.641

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74972472153→33.5715 Å / SU ML: 0.224356588544 / Cross valid method: THROUGHOUT / σ(F): 1.33787791182 / Phase error: 28.414798127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233146364321 1614 10.0018590816 %
Rwork0.203370558466 14523 -
obs0.206365317843 16137 85.9585575028 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.8214989485 Å2
Refinement stepCycle: LAST / Resolution: 1.74972472153→33.5715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 0 68 1343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006302414775361365
X-RAY DIFFRACTIONf_angle_d0.7874303796511863
X-RAY DIFFRACTIONf_chiral_restr0.0466051309519203
X-RAY DIFFRACTIONf_plane_restr0.00412347643657239
X-RAY DIFFRACTIONf_dihedral_angle_d11.2840935882822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74972472153-1.80120.398362910731500.298279002452473X-RAY DIFFRACTION33.8950097213
1.8012-1.85930.348612096361760.29457701481647X-RAY DIFFRACTION47.5971033575
1.8593-1.92580.311375633892980.276019336672835X-RAY DIFFRACTION60.5058365759
1.9258-2.00290.2977168098291300.2736513019641217X-RAY DIFFRACTION87.4107722258
2.0029-2.0940.2912551214911570.2726046497021399X-RAY DIFFRACTION100
2.094-2.20440.2912356082111500.2475030254471373X-RAY DIFFRACTION100
2.2044-2.34250.2691531413611510.2335231198791413X-RAY DIFFRACTION100
2.3425-2.52330.2802653020421580.2368820736941409X-RAY DIFFRACTION100
2.5233-2.77710.2593364117751520.2316404648631406X-RAY DIFFRACTION100
2.7771-3.17870.2200230298451570.2206704599671421X-RAY DIFFRACTION100
3.1787-4.00380.2115370951811620.1801093027051432X-RAY DIFFRACTION100
4.0038-33.57150.2009885313351730.1653291709151498X-RAY DIFFRACTION99.8804542738
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)
11.40833410154-1.00119911304-0.5726594588965.40704249294-0.8551405568965.39254520510.03439496932280.866407315090.364187438456-1.319734195440.2893787576520.553568607028-0.556828986014-0.321827919479-0.3221786884310.680304461151-0.119439935347-0.05023428339640.6468873193310.1191156834940.349416473622-21.990676196127.2707728558-3.07342054101
24.82109692331-1.75802748914-1.834959384683.34306112933-1.06751107712.179286929820.1244705537921.47678407179-0.805949350689-0.887966481073-0.3222312095860.6395812923830.5685340410790.09240101553950.2189461839620.924156956992-0.0343084308585-0.04626370769470.879830268148-0.121351994080.435110994225-19.702573905318.5390038131-6.98083128156
34.771646174090.213131875153-0.1001022230174.394433632610.7515050716613.35299837504-0.08067558360610.3092880921580.291186435025-0.6747079035260.1750338634750.8070358524310.222906407749-0.525887260836-0.08436483997350.454209809555-0.0797326377088-0.08811151020610.5038580936390.06827315636320.374755323332-25.43266320723.90526883453.22566096784
43.844978846131.15735793554-0.8121981691890.8805713873940.8849929472072.138041246080.0275613378280.606751788165-0.661368848774-0.156616628816-0.0713079946881-0.4195773159220.3193225768420.6733098461560.04727877339650.2359451155490.1164222560430.1060776713910.5114499557020.0618114608190.424289496937-1.8287134290521.056463584616.9468981724
52.09045951279-0.699859080388-1.382602929132.783634577340.7076788753724.48229903375-0.185874804177-0.41866469596-0.801685699159-0.04871420621410.014323989655-0.1179158360390.7891820056280.5038399441940.1139875752390.3161487765980.06607599456540.09536842608760.3424442368880.0669087489270.403837396722-10.806183376415.267416933316.79129876
62.111116667953.62404555471-0.1819562143766.7659800556-1.411420240074.323529602250.1954780931450.5693258848010.705406317246-0.279391081635-0.025394719280.49883163595-0.02230529254690.6417276067980.1151096437270.3379967183550.03721584953990.1427440151910.4322560609240.0484240021220.377261063779-10.07399131422.13304724129.34574357027
75.30516877613-1.169314011640.7445911815024.351635489931.047822188895.62622813126-0.165767087751.04125752228-0.186956926649-0.579749054686-0.176392758150.262584902543-0.2163882749430.5361585869360.3316238695280.4989433560470.06501765689090.09569272572220.5609483020410.03167719462520.306874531278-8.5308844780221.17839420774.79370010226
81.13359617881.409906912380.2425894400441.77792452630.3633755343346.118588012740.1181062575760.762120452954-0.22132657572-0.2804596037110.987884612814-0.2384607143250.2349429439730.6911878073621.951114962650.5700686518520.1785611803570.4321081897071.277515131580.04416638993360.3187157653770.565388048519.0164995822-0.163234095862
99.215277582812.14895476667-3.974110289966.71328323844-2.998960847769.23447174919-0.106492727560.941665347195-1.00366792042-0.06886027498280.2478995744530.05064310023191.015992508770.0540048087624-0.1418503189020.5055775271690.08495192908110.08950378824570.43162556537-0.0707382917040.581081138488-9.0428564156910.702063354311.6164522157
103.835590142650.878439590175-1.173561170912.56646452428-0.4812857476440.920605547401-0.06366223746650.612863918373-0.141251829584-0.3327586063450.382567656648-0.895951943150.3489364301511.561028884210.2868741986730.3565380124550.05058332519210.3239479649830.956037965085-0.08174419712510.5724072597971.9805030067918.11591651499.26536896373
113.165239546240.4893701992351.323384951682.374521895840.9648281922212.23168846367-0.1101023716820.6389718312440.164918272279-0.1274306732750.0945011308197-0.114343862882-0.1056953056180.3331051653250.05371072529830.2660730201460.003048238418690.05646302181230.3463233741760.08300989290360.323348070784-10.887719444525.736682891114.0609040105
120.9088949662121.27947137885-0.3371194136031.77994965736-0.4635252421670.118023862483-0.1022916322940.972595455692-0.203660978388-0.5413518290310.110457692637-0.622344483435-0.6874547493621.33766780265-0.1425037955360.070345398127-0.1074750026350.2766560039561.056651876670.05704781320140.5087153959686.5695600655425.41787617714.2773192516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 63 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 17 )
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 39 )
7X-RAY DIFFRACTION7chain 'B' and (resid 40 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 66 )
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 76 )
10X-RAY DIFFRACTION10chain 'B' and (resid 77 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 104 )
12X-RAY DIFFRACTION12chain 'B' and (resid 105 through 111 )

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