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- PDB-4yk2: Crystal Structure of the BID Domain of Bep9 from Bartonella clarr... -

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Basic information

Entry
Database: PDB / ID: 4yk2
TitleCrystal Structure of the BID Domain of Bep9 from Bartonella clarridgeiae
ComponentsBartonella effector protein (Bep) substrate of VirB T4SS
KeywordsPROTEIN BINDING / SSGCID / Bartonella clarridgeiae / Bep9 / VirB-translocated Bartonella effector protein / BID domain / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyBartonella effector protein, BID domain / BID domain of Bartonella effector protein (Bep) / Bartonella effector protein (Bep) substrate of VirB T4SS
Function and homology information
Biological speciesBartonella clarridgeiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Structure / Year: 2017
Title: The BID Domain of Type IV Secretion Substrates Forms a Conserved Four-Helix Bundle Topped with a Hook.
Authors: Stanger, F.V. / de Beer, T.A. / Dranow, D.M. / Schirmer, T. / Phan, I. / Dehio, C.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bartonella effector protein (Bep) substrate of VirB T4SS
B: Bartonella effector protein (Bep) substrate of VirB T4SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,28210
Polymers33,5482
Non-polymers7358
Water3,081171
1
A: Bartonella effector protein (Bep) substrate of VirB T4SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2546
Polymers16,7741
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bartonella effector protein (Bep) substrate of VirB T4SS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0284
Polymers16,7741
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.680, 62.310, 71.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-410-

HOH

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Components

#1: Protein Bartonella effector protein (Bep) substrate of VirB T4SS / BepE


Mass: 16773.988 Da / Num. of mol.: 2 / Fragment: BID domain (UNP residues 64-201)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella clarridgeiae (bacteria) / Strain: CIP 104772 / 73 / Gene: BARCL_1032 / Plasmid: BaclA.17330.i.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E6YIM5
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1:1 24.7 mg/mL protein and MCSG1(c8) (0.2 M ammonium sulfate, 0.1 M sodium citrate/HCl, pH 5.6, 25% PEG4000), cryoprotectant: 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2014 / Details: Beryllium Lenses
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 21863 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 28.3 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.068 / Χ2: 0.977 / Net I/σ(I): 19.33 / Num. measured all: 106806
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.05-2.10.890.5483.187902160815970.61199.3
2.1-2.160.9330.4334.117613155215440.48399.5
2.16-2.220.9540.3524.977536153315250.39399.5
2.22-2.290.970.2696.237243146414580.399.6
2.29-2.370.9750.237.346990142514190.25699.6
2.37-2.450.9740.2018.236731137113690.22599.9
2.45-2.540.9830.15910.146724136813660.17799.9
2.54-2.650.990.12312.826323128712860.13899.9
2.65-2.760.9930.10315.056104124312420.11599.9
2.76-2.90.9960.07918.95817118411800.08899.7
2.9-3.060.9970.06322.495555113611330.0799.7
3.06-3.240.9980.05226.855227107210650.05899.3
3.24-3.470.9980.0432.884991103110270.04599.6
3.47-3.740.9980.03439.145409429330.03899
3.74-4.10.9990.02944.6442368818750.03399.3
4.1-4.580.9990.02647.9137727997910.02999
4.58-5.290.9990.02348.9834007227160.02699.2
5.29-6.480.9990.02841.7228226186020.03197.4
6.48-9.1710.02251.8121914934760.02496.6
9.170.9990.01859.5910893032590.02185.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4YK1

4yk1


Resolution: 2.05→46.844 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1082 4.96 %
Rwork0.1711 20744 -
obs0.1732 21826 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.44 Å2 / Biso mean: 37.2438 Å2 / Biso min: 16.06 Å2
Refinement stepCycle: final / Resolution: 2.05→46.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 39 171 1886
Biso mean--110.7 41.36 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071795
X-RAY DIFFRACTIONf_angle_d0.9832426
X-RAY DIFFRACTIONf_chiral_restr0.046267
X-RAY DIFFRACTIONf_plane_restr0.004316
X-RAY DIFFRACTIONf_dihedral_angle_d14.47701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.14330.24461340.20562563269799
2.1433-2.25630.23121300.1792544267499
2.2563-2.39760.21891350.17325692704100
2.3976-2.58270.2261420.173425612703100
2.5827-2.84260.22111310.177726012732100
2.8426-3.25390.26581410.177925932734100
3.2539-4.09920.20641330.15822621275499
4.0992-46.85620.17411360.16642692282897
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)
10.2880.1362-0.1820.27390.27750.4703-0.11460.35620.0176-0.21730.1507-0.1710.09520.3185-0.0230.28950.03220.01850.26470.01990.201335.514435.7765-14.2421
20.58940.2278-0.0310.7755-0.44431.09910.0509-0.01330.06550.0673-0.1335-0.0009-0.0987-0.1072-0.00010.1660.0521-0.02420.1849-0.01770.221731.29241.89283.6984
30.6011-0.0321-0.61960.6018-0.45961.0295-0.05010.12680.225-0.3205-0.11840.1265-0.2504-0.1574-0.00660.23780.0526-0.05940.22070.03420.268932.07844.394-5.4766
40.5138-0.32690.58210.1948-0.34350.5537-0.1007-0.2292-0.02430.2267-0.04470.09340.0280.0515-0.00960.3212-0.0614-0.00280.33420.00730.208431.718432.126130.0796
50.04690.0648-0.03830.1012-0.10330.2210.0399-0.12720.1153-0.18760.0952-0.04440.5839-0.32540.00270.2422-0.0014-0.03390.2866-0.0340.240528.74127.352712.3608
60.1262-0.0255-0.09490.00620.01890.0678-0.08870.01630.07250.3389-0.0973-0.2028-0.1460.50440.00040.3061-0.0622-0.06360.34130.04390.295835.892938.051717.2641
70.17280.2783-0.24220.4369-0.3840.3341-0.0179-0.07890.25810.0213-0.12440.4669-0.4219-0.1939-0.00030.30240.0184-0.00520.2598-0.04990.260424.742741.280313.3742
80.20060.09880.1080.2068-0.15290.24280.1563-0.0946-0.0008-0.0365-0.05350.24560.3931-0.1775-0.00380.3052-0.0926-0.03380.2802-0.04450.318314.087926.92888.0096
90.9001-0.46230.24541.80160.27640.1791-0.283-0.22290.12850.4993-0.05160.1062-0.33610.0424-0.19110.3614-0.1337-0.01210.3477-0.02450.204127.818737.772124.823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 73 through 103 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 150 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 179 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 73 through 102 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 103 through 109 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 119 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 120 through 136 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 137 through 159 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 178 )B0

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