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- PDB-7sh3: Crystal Structure of a VirB8-like Protein of Type IV Secretion Sy... -

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Basic information

Entry
Database: PDB / ID: 7sh3
TitleCrystal Structure of a VirB8-like Protein of Type IV Secretion System from Rickettsia typhi in Complex with a Synthetic VirB8 Miniprotein Binder
Components
  • Synthetic VirB8 Miniprotein Binder
  • VirB8-like protein of type IV secretion system
KeywordsPROTEIN TRANSPORT / SSGCID / synthetic / miniprotein binder / minibinder / VirB8 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyBacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / membrane / VirB8-like protein of type IV secretion system
Function and homology information
Biological speciessynthetic construct (others)
Rickettsia typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of a VirB8-like Protein of Type IV Secretion System from Rickettsia typhi in Complex with a Synthetic VirB8 Miniprotein Binder
Authors: DeBouver, N.D. / Bera, A.K. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synthetic VirB8 Miniprotein Binder
B: VirB8-like protein of type IV secretion system


Theoretical massNumber of molelcules
Total (without water)28,8252
Polymers28,8252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-12 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.260, 71.480, 155.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Synthetic VirB8 Miniprotein Binder


Mass: 7615.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Gene: synthetic / Plasmid: SycoA.20508.e.PG1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein VirB8-like protein of type IV secretion system


Mass: 21209.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia typhi (strain ATCC VR-144 / Wilmington) (bacteria)
Strain: ATCC VR-144 / Wilmington / Gene: RT0278 / Plasmid: RityA.18390.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q68X84

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: RityA.18390.a.B2 + SycoA.20508.e.PG1 [Barcode: 320527g9, PuckID: oce7-3, Cryo: 15% EG, Concentration: 9.9 mg/mL] 100mM Sodium acetate/Hydrochloric acid pH 4.6, 25% (w/v) PEG 4000, 200mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 15, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3→44.69 Å / Num. obs: 6672 / % possible obs: 99.8 % / Redundancy: 5.897 % / Biso Wilson estimate: 86.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.082 / Χ2: 0.889 / Net I/σ(I): 13.47 / Num. measured all: 39344
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.086.0950.6772.5229444844830.9380.7499.8
3.08-3.166.1270.563.0328554694660.9620.61399.4
3.16-3.256.0860.4783.5727454524510.9830.52499.8
3.25-3.356.0730.3484.6627634554550.9860.381100
3.35-3.466.0260.2415.7525794284280.9970.264100
3.46-3.596.0470.2256.9625824284270.9940.24799.8
3.59-3.726.0080.1638.3723133853850.9950.178100
3.72-3.875.9490.12610.3724274084080.9970.139100
3.87-4.055.9270.12211.6121873693690.9950.134100
4.05-4.245.8020.09313.920833603590.9970.10299.7
4.24-4.475.7810.06416.9620293513510.9990.07100
4.47-4.745.790.05620.8919053293290.9990.061100
4.74-5.075.740.05422.1317453043040.9990.059100
5.07-5.485.7940.05222.3816572862860.9990.057100
5.48-65.7880.05721.7515862742740.9990.063100
6-6.715.7550.05424.8813872412410.9980.059100
6.71-7.755.650.04230.0612602232230.9990.047100
7.75-9.495.6070.02937.9310711911910.9980.033100
9.49-13.425.3640.02540.678101511510.9990.028100
13.42-44.694.5710.02436.8941698910.9990.02892.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXdev-4274refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3V

4o3v


Resolution: 3→44.69 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3061 676 10.24 %
Rwork0.2385 5924 -
obs0.2453 6600 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.91 Å2 / Biso mean: 129.2413 Å2 / Biso min: 91.9 Å2
Refinement stepCycle: final / Resolution: 3→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 0 0 1534
Num. residues----188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.230.45731350.40251137127298
3.23-3.560.38211380.31521150128898
3.56-4.070.34371280.24731182131099
4.07-5.130.25671360.197511841320100
5.13-44.690.27771390.21591271141099
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)
16.78362.46660.30836.2225-1.48923.85020.8603-0.5959-0.7363-0.502-0.7584-0.7551-0.38620.3463-0.31381.1202-0.23110.0422.5606-0.23440.69883.85190.555824.4836
29.2735-1.8569-6.50947.05281.4167.75651.0679-0.95360.1434-0.1919-0.5767-1.1213-1.51960.6145-0.5851.2632-0.1799-0.05722.1342-0.04440.95258.06594.181530.5232
34.7129-4.8997-3.21289.53971.90843.9812-0.8045-0.6982-2.2553-0.5715-0.68081.0998-0.37160.2540.57560.8069-0.1256-0.00891.5442-0.15821.04-0.2511-8.3275-1.5994
45.8069-1.6580.80083.92872.87516.15290.2931-0.52620.35050.2184-0.6691-0.6259-0.38060.45080.53210.8337-0.08170.00911.2637-0.05720.84992.2626-0.982814.3661
54.9912-0.2156-0.5241.06671.41237.8114-0.69560.63380.48580.08060.04750.55390.6433-1.01690.28240.7925-0.02930.03161.6729-0.15440.9889-7.8272.95138.9101
68.8412-2.3153-1.13088.18851.36025.89590.36520.85130.9431-0.1238-0.4676-0.22750.08661.13130.38240.6496-0.0983-0.07921.5002-0.01950.6139-1.7651.27521.404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 25 )A4 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 66 )A26 - 66
3X-RAY DIFFRACTION3chain 'B' and (resid 31 through 49 )B31 - 49
4X-RAY DIFFRACTION4chain 'B' and (resid 50 through 86 )B50 - 86
5X-RAY DIFFRACTION5chain 'B' and (resid 87 through 106 )B87 - 106
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 162 )B107 - 162

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