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- PDB-4wgj: Crystal Structure of BepC protein (VirB-translocated Bartonella e... -

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Basic information

Entry
Database: PDB / ID: 4wgj
TitleCrystal Structure of BepC protein (VirB-translocated Bartonella effector protein) with bound AMPPNP from Bartonella tribocorum
ComponentsBepC protein
KeywordsTRANSFERASE / VirB-translocated Bartonella effector protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GLYCINE / protein adenylyltransferase
Similarity search - Component
Biological speciesBartonella tribocorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / reflns_shell / software
Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
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
Revision 1.3Sep 27, 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: BepC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9955
Polymers26,2771
Non-polymers7184
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-3 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.330, 92.020, 45.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is a monomer

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Components

#1: Protein BepC protein


Mass: 26276.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella tribocorum (bacteria) / Strain: CIP 105476 / IBS 506 / Gene: bepC, BT_1704 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9IWP7
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: at 22.75mg/ml, incubated with 8mM each MgCl2 and AMPPNP, then 1:1 with Morpheus(H2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.02M each sodium L-glutamate, DL-alanine, ...Details: at 22.75mg/ml, incubated with 8mM each MgCl2 and AMPPNP, then 1:1 with Morpheus(H2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.02M each sodium L-glutamate, DL-alanine, glycine, DL-lysine, DL-serine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 12, 2014
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 28113 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 15.95 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.056 / Χ2: 0.947 / Net I/σ(I): 20.88 / Num. measured all: 126835
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.7420.7070.4652.14100207919140.60692.1
1.74-1.790.8010.4372.75420198219630.54399
1.79-1.840.8490.3693.345591195419440.45499.5
1.84-1.90.9020.3024.15669189318830.36899.5
1.9-1.960.920.2514.965747183518330.30399.9
1.96-2.030.9560.1836.965884179517920.21999.8
2.03-2.110.9740.1479.16029172617200.17499.7
2.11-2.190.9850.1212.937128169016890.13899.9
2.19-2.290.9910.10116.527355158815880.114100
2.29-2.40.9930.08619.117472152815280.096100
2.4-2.530.9960.07122.867557146114600.07999.9
2.53-2.690.9970.0626.867831139613950.06799.9
2.69-2.870.9980.05332.68523130713070.057100
2.87-3.10.9990.04539.628766122312230.048100
3.1-3.40.9990.03546.138084113111300.03899.9
3.4-3.810.02759.397319103010310.029100
3.8-4.3910.02566.564739219210.027100
4.39-5.380.9990.02465.2554877917910.026100
5.38-7.60.9990.02954.7242336276270.032100
7.60.9990.02271.2921673753740.02599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
StructureStudio2.5.6data collection
PHENIX(phenix.refine: dev_1803)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
ARPArpWarpmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N67

4n67


Resolution: 1.7→46.01 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1929 1384 4.92 %Random selection
Rwork0.1639 26729 --
obs0.1653 28113 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.56 Å2 / Biso mean: 21.5511 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 1.7→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 45 231 1916
Biso mean--32.16 32.57 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061754
X-RAY DIFFRACTIONf_angle_d1.0112385
X-RAY DIFFRACTIONf_chiral_restr0.039251
X-RAY DIFFRACTIONf_plane_restr0.005312
X-RAY DIFFRACTIONf_dihedral_angle_d12.89638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.76080.30641520.25152445259794
1.7608-1.83130.25911240.22612657278199
1.8313-1.91460.24621420.204926562798100
1.9146-2.01560.20931310.173726452776100
2.0156-2.14190.17271530.160126342787100
2.1419-2.30720.17931310.152526802811100
2.3072-2.53940.19971180.15627022820100
2.5394-2.90680.19851570.158426882845100
2.9068-3.6620.16171450.156127342879100
3.662-46.02680.17581310.146528883019100
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)
12.4203-0.977-0.73344.47651.59451.5665-0.0557-0.257-0.2390.33860.0938-0.18890.88520.4015-0.00170.29330.049-0.00530.14230.01960.197739.47415.1919-8.8646
22.5365-0.88310.2122.6278-0.83532.223-0.00020.3121-0.1753-0.4565-0.0927-0.40070.2670.46730.10880.20910.01570.05050.2414-0.05030.172944.10114.2074-24.2777
32.103-0.10520.42985.0077-0.16073.011-0.00410.12710.0919-0.0882-0.00530.1828-0.0766-0.0275-0.00370.0523-0.0047-0.00630.10670.00230.073434.962621.9897-18.9602
46.03122.75570.51996.01251.23042.89820.0961-0.2579-0.17870.1191-0.10450.01020.2844-0.1170.00320.133-0.010.02220.09630.01760.070434.380913.6864-4.8566
51.73910.7302-0.25953.2589-1.78793.47240.0276-0.0310.23290.24610.01980.1436-0.39640.0863-0.01910.1311-0.00620.01520.0845-0.02730.116143.442734.1997-10.299
61.30750.41040.02880.880.15690.0723-0.0080.00750.02880.0147-0.0351-0.07890.00020.10950.04940.1154-0.0020.00510.13820.00530.094649.358127.0669-15.4587
72.8962-1.0312.2783.8623-1.23485.99030.08950.39570.4054-0.219-0.03940.0848-0.15680.24530.02110.1349-0.02870.01460.19030.04170.139654.873535.1686-19.3501
80.98742.92553.15328.90229.26952-0.15710.80524.9711.0893-0.8121-1.1591-4.5545-1.63171.00320.46280.1609-0.00190.6341-0.07961.198653.206321.7543-18.3612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:22 )A0 - 22
2X-RAY DIFFRACTION2( CHAIN A AND RESID 23:43 )A23 - 43
3X-RAY DIFFRACTION3( CHAIN A AND RESID 44:73 )A44 - 73
4X-RAY DIFFRACTION4( CHAIN A AND RESID 74:93 )A74 - 93
5X-RAY DIFFRACTION5( CHAIN A AND RESID 94:145 )A94 - 145
6X-RAY DIFFRACTION6( CHAIN A AND RESID 146:194 )A146 - 194
7X-RAY DIFFRACTION7( CHAIN A AND RESID 195:209 )A195 - 209
8X-RAY DIFFRACTION8( CHAIN A AND RESID 303:303 )A303

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