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- PDB-4m16: Crystal Structure of the N-terminal Fic Domain of Bartonella effe... -

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Basic information

Entry
Database: PDB / ID: 4m16
TitleCrystal Structure of the N-terminal Fic Domain of Bartonella effector protein (Bep); substrate of VirB T4SS (VirB-translocated Bep effector protein) from Bartonella sp. AR 15-3
ComponentsBartonella effector protein (Bep) substrate of VirB T4SS
KeywordsCELL ADHESION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Fic domain / cell filamentation
Function / homology
Function and homology information


protein adenylyltransferase / regulation of cell division / nucleotidyltransferase activity / ATP binding
Similarity search - Function
BepA, intracellular delivery domain / Intracellular delivery domain / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
protein adenylyltransferase
Similarity search - Component
Biological speciesBartonella sp. AR 15-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Microorganisms / Year: 2021
Title: Evolutionary Diversification of Host-Targeted Bartonella Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module.
Authors: Schirmer, T. / de Beer, T.A.P. / Tamegger, S. / Harms, A. / Dietz, N. / Dranow, D.M. / Edwards, T.E. / Myler, P.J. / Phan, I. / Dehio, C.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / Item: _citation.page_first
Revision 1.3Sep 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,1982
Polymers28,1361
Non-polymers621
Water4,882271
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.240, 47.480, 67.970
Angle α, β, γ (deg.)90.000, 105.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28136.186 Da / Num. of mol.: 1 / Fragment: UNP residues 9-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella sp. AR 15-3 (bacteria) / Gene: BAR15_120228 / Production host: Escherichia coli (E. coli) / References: UniProt: E6YQQ1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG1(a1): 0.1 M HEPES/NaOH, pH 7.5, 20% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 21300 / Num. obs: 21213 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 28.044 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.5522.295937156199.8
1.9-1.950.4243.266315151999.5
1.95-2.010.3294.216169147999.5
2.01-2.070.2675.215955142499.7
2.07-2.140.2136.555843139999.9
2.14-2.210.1648.415648134999.9
2.21-2.290.13510.295362128699.6
2.29-2.390.1111.975306127799.5
2.39-2.490.113.675054120699.6
2.49-2.620.07916.644787114399.9
2.62-2.760.06419.834573109199.4
2.76-2.930.05324.864303103899.3
2.93-3.130.04229.44410898799.7
3.13-3.380.03337.33375290399.4
3.38-3.70.02743.72336082498.8
3.7-4.140.02351.08313676599.7
4.14-4.780.0255.39280668299.9
4.78-5.850.02153.35235958099.5
5.85-8.270.02154.71795449100
8.270.01564.6291625196.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.85 Å38.75 Å
Translation1.85 Å38.75 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LU4

4lu4


Resolution: 1.85→38.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1945 / WRfactor Rwork: 0.1529 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8646 / SU B: 5.641 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1317 / SU Rfree: 0.1289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 1091 5.1 %RANDOM
Rwork0.164 ---
obs0.1665 21205 99.63 %-
all-22296 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.1 Å2 / Biso mean: 24.264 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å2-0.61 Å2
2---1.11 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 4 271 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191893
X-RAY DIFFRACTIONr_bond_other_d0.0010.021759
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.942558
X-RAY DIFFRACTIONr_angle_other_deg0.86534054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.85524.38898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93815330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.758158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022169
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_mcbond_it0.9121.214911
X-RAY DIFFRACTIONr_mcbond_other0.9071.213910
X-RAY DIFFRACTIONr_mcangle_it1.4341.8131140
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 71 -
Rwork0.248 1478 -
all-1549 -
obs--99.55 %
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)
10.52050.14240.82220.8377-0.96676.5551-0.1036-0.03420.0432-0.02080.0585-0.0565-0.0251-0.28020.04520.13660.011-0.01210.056-0.03260.051423.1166-4.518870.8024
22.95632.69551.42215.46954.05566.46470.05050.07770.06120.223-0.11640.20750.1026-0.27180.06590.1330.04710.00280.05140.01470.07520.4315-1.76890.8917
30.37260.09890.2191.69710.44420.882-0.00290.01840.00880.00720.072-0.11530.01530.0863-0.06910.09020.01020.00290.065-0.0090.056827.693313.684183.3106
41.24010.00570.9343.4275-2.3199.81880.08040.0311-0.0880.14830.12220.3772-0.0835-0.5931-0.20260.04480.01230.00950.09760.01930.12411.776515.553587.1333
51.0306-0.35641.01082.15120.072410.1064-0.02340.07260.04970.03890.02950.4203-0.5929-0.0433-0.00610.11620.031-0.00820.0986-0.01660.152613.156725.723180.1648
64.6429-2.7639-8.02742.84015.531114.4411-0.0927-0.4024-0.02150.09570.0699-0.2060.21010.60810.02280.1331-0.00260.02020.14640.04630.2111.290625.4972102.7931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 27
2X-RAY DIFFRACTION2A28 - 50
3X-RAY DIFFRACTION3A51 - 177
4X-RAY DIFFRACTION4A178 - 195
5X-RAY DIFFRACTION5A196 - 210
6X-RAY DIFFRACTION6A211 - 225

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