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- PDB-4yk3: Crystal Structure of the BID Domain of BepE from Bartonella henselae -

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Basic information

Entry
Database: PDB / ID: 4yk3
TitleCrystal Structure of the BID Domain of BepE from Bartonella henselae
ComponentsBepE protein
KeywordsPROTEIN BINDING / SSGCID / Bartonella henselae / BepE / VirB-translocated Bartonella effector protein / BID domain / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyBepE protein / BepE protein
Function and homology information
Biological speciesBartonella henselae str. Houston-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Sep 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: BepE protein
B: BepE protein
C: BepE protein
D: BepE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0017
Polymers66,8154
Non-polymers1863
Water2,234124
1
A: BepE protein


Theoretical massNumber of molelcules
Total (without water)16,7041
Polymers16,7041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BepE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7662
Polymers16,7041
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BepE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8283
Polymers16,7041
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BepE protein


Theoretical massNumber of molelcules
Total (without water)16,7041
Polymers16,7041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.070, 77.420, 67.510
Angle α, β, γ (deg.)90.000, 93.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BepE protein / Bartonella effector protein


Mass: 16703.797 Da / Num. of mol.: 4 / Fragment: BID domain (UNP residues 132-268)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae str. Houston-1 (bacteria)
Gene: bepE / Plasmid: BaheA.17330.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5QT01, UniProt: A0A0R4J6H0*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 28.3 mg/mL protein and MCSG1(a9) (25% PEG3350, 0.1 M HEPES/NaOH, pH 7.5, 0.2 M magnesium chloride), 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 20, 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: 2.2→50 Å / Num. obs: 30337 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 39.64 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.05 / Χ2: 0.953 / Net I/σ(I): 23.49 / Num. measured all: 140015
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.260.8420.5292.9110368223322300.59699.9
2.26-2.320.8770.4233.6810087217321670.47799.7
2.32-2.390.9150.3534.279800211021050.39899.8
2.39-2.460.9320.2855.329569205820570.322100
2.46-2.540.9650.2146.99336200420010.24199.9
2.54-2.630.9790.1688.829072194919500.19100
2.63-2.730.9840.14210.588670186218550.1699.6
2.73-2.840.990.10813.538354179617940.12299.9
2.84-2.970.9950.07817.748054173517310.08899.8
2.97-3.110.9970.06122.097708165516540.06999.9
3.11-3.280.9980.04628.577174154415400.05299.7
3.28-3.480.9990.03735.486875149014870.04299.8
3.48-3.720.9990.02844.616456140614030.03199.8
3.72-4.020.9990.02450.995923130713030.02799.7
4.02-4.40.9990.02257.65485120612030.02599.8
4.4-4.920.9990.0260.714890108710830.02399.6
4.92-5.6810.0256.6943789769740.02399.8
5.68-6.9610.0259.5336118078070.022100
6.96-9.8410.01571.2628406526520.017100
9.840.9990.01575.2713653613410.01794.5

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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 4YK2

4yk2


Resolution: 2.2→42.611 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1509 4.98 %
Rwork0.1828 28822 -
obs0.1849 30331 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.72 Å2 / Biso mean: 54.0423 Å2 / Biso min: 21.73 Å2
Refinement stepCycle: final / Resolution: 2.2→42.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 12 124 3324
Biso mean--61.34 48.63 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083265
X-RAY DIFFRACTIONf_angle_d0.9744428
X-RAY DIFFRACTIONf_chiral_restr0.044502
X-RAY DIFFRACTIONf_plane_restr0.004592
X-RAY DIFFRACTIONf_dihedral_angle_d14.3451165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.27110.26651360.231526002736100
2.2711-2.35230.27731290.222326092738100
2.3523-2.44640.28261390.212626062745100
2.4464-2.55780.24871400.198626042744100
2.5578-2.69260.25651370.202426292766100
2.6926-2.86130.24671420.210125942736100
2.8613-3.08210.2431350.201426172752100
3.0821-3.39220.26551360.190626322768100
3.3922-3.88270.21561390.165626272766100
3.8827-4.89070.19891340.1526332767100
4.8907-42.61850.18161420.17962671281399
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)
11.85621.9749-0.19777.45524.96214.8197-0.04280.2246-0.26310.16940.0628-0.20650.97950.3281-0.23770.59090.05680.02170.3338-0.01360.35893.616813.316915.829
29.20376.37435.14125.32314.89145.2032-0.3320.1345-0.87780.6307-0.17140.47811.3893-1.00190.54510.8835-0.190.25770.5523-0.09610.6116-4.886111.351716.9212
37.6079-1-0.69276.61914.2466.3242-0.00030.86590.0205-0.9052-0.28340.7504-0.3262-0.78180.34390.485-0.0096-0.03810.33170.01710.346-6.589323.364715.7914
46.9215.63291.29968.26323.66984.63720.2221-0.87670.41740.3407-0.30240.27850.12380.27290.20710.3304-0.042-0.01740.3299-0.09790.2964.706433.15730.9247
53.96021.65842.01953.35512.64523.21480.04460.5377-0.1594-0.27690.1538-0.15180.11820.3743-0.11730.3982-0.04510.07150.3501-0.03480.27822.882220.956612.2916
64.79123.4848-0.25015.27544.31127.33-0.2433-1.597-0.15120.8284-0.73290.68742.5555-0.43540.75991.0143-0.08250.12990.6193-0.07970.45943.07230.2135-1.0699
74.45671.99890.76353.8443-0.35833.16010.2505-0.8755-0.11940.7961-0.0049-0.42320.13950.7247-0.24550.41450.0305-0.07150.5899-0.10960.315810.57111.898968.7197
85.3912.37061.98317.215.07519.3865-0.11620.24130.3889-0.26030.2393-0.6662-0.88661.2356-0.04210.4075-0.06910.04080.5182-0.02640.375612.240515.826858.9669
99.87645.64182.26266.72432.0144.069-0.3160.50650.0587-0.10990.26630.10040.00880.51620.05240.42120.02150.00030.2754-0.05320.25651.41170.366647.6846
104.60311.91292.52274.10414.07157.7646-0.1154-0.31730.75050.067-0.29510.6784-0.74090.02810.40740.4590.03430.01930.3101-0.0540.25263.791614.581563.266
114.70464.88893.08568.9472-1.62738.12920.43860.3577-0.86360.69841.3312-0.2517-1.9807-0.0641-1.06790.99570.32690.54970.88630.25791.1318-19.727447.584829.048
121.16990.7041-1.26151.59960.03345.033-0.2192-0.51811.2660.51560.53570.0253-0.2228-0.5182-0.21070.36620.06420.07220.3686-0.00840.6167-14.047932.652441.6023
136.36-2.49062.16466.8375-3.63543.43360.09250.2990.74110.27350.121-0.0644-1.34190.1955-0.16790.37650.01810.10120.46650.03130.675-9.607135.455132.7534
146.1851-3.36610.93097.8704-2.52288.2101-0.10380.78770.2492-0.35440.28060.3289-0.1139-1.1139-0.33880.352-0.06470.01880.48340.13840.4269-13.292525.543628.7654
154.9496-2.24491.35989.3298-5.02312.62760.0929-0.3115-0.1448-0.2715-0.3874-0.35451.32580.79010.40560.58940.1512-0.05490.38790.00490.2627-1.21816.324443.2241
168.3164-6.80854.02698.0945-3.78847.36430.16170.0530.2063-0.05290.29110.76160.3656-0.7879-0.36330.2687-0.02990.09040.49080.08380.5306-16.678626.793638.5941
176.8832-2.35510.72554.5363-1.6524.7564-0.2196-1.2671-0.60810.36490.16980.06460.23430.3462-0.05030.27020.06490.00360.48810.04740.329318.522138.976343.6906
184.9264-4.80692.31878.5995-2.60266.57950.2260.7368-0.1857-0.5565-0.67-0.87770.68210.78080.25560.28610.05230.06330.4060.01060.589921.975237.861538.1804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 142 through 177 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 187 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 204 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 218 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 251 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 261 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 144 through 171 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 172 through 204 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 218 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 219 through 250 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 141 through 153 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 154 through 171 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 172 through 187 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 188 through 204 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 205 through 218 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 219 through 247 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 149 through 218 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 219 through 248 )D0

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