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- PDB-4n67: Crystal Structure of the N-terminal Fic Domain of a Putative Cell... -

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Basic information

Entry
Database: PDB / ID: 4n67
TitleCrystal Structure of the N-terminal Fic Domain of a Putative Cell Filamentation protein (VirB-translocated Bep effector protein) with bound ADP from Bartonella quintana
ComponentsPutative cell filamentation protein
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / cell filamentation / adenylylation / ampylation
Function / homology
Function and homology information


Bartonella effector protein, BID domain / BID domain of Bartonella effector protein (Bep) / 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. ...Bartonella effector protein, BID domain / BID domain of Bartonella effector protein (Bep) / 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
ADENOSINE-5'-DIPHOSPHATE / Putative cell filamentation protein / Putative cell filamentation protein
Similarity search - Component
Biological speciesBartonella quintana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Structure summary
Revision 1.2Sep 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 1.3Sep 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: Putative cell filamentation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8983
Polymers26,4461
Non-polymers4522
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.450, 64.070, 97.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative cell filamentation protein


Mass: 26446.338 Da / Num. of mol.: 1 / Mutation: M2, L65N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: BQ10650 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FYV8, UniProt: A0A0H3LV04*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG+(g7): 01.M Succinic Acid, pH=7.0, 15% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 37687 / Num. obs: 37518 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.71
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.590.493.51199.3
1.59-1.630.3884.58199.2
1.63-1.680.3145.6199.8
1.68-1.730.2337.53199.5
1.73-1.790.1899.05199.6
1.79-1.850.15111.08199.7
1.85-1.920.11813.891100
1.92-20.0917.88199.8
2-2.090.07321.46199.9
2.09-2.190.05826.68199.8
2.19-2.310.05129.66199.7
2.31-2.450.04532.73199.9
2.45-2.620.0437.2199.5
2.62-2.830.03740.82199.6
2.83-3.10.03245.391100
3.1-3.470.0349.281100
3.47-40.02754.75199.6
4-4.90.02555.54199.5
4.9-6.930.02653.48199.2
6.930.02652.52190.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.55 Å40.45 Å
Translation1.55 Å40.45 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 2JK8

2jk8


Resolution: 1.55→19.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 2.443 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0757 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19419 1874 5 %RANDOM
Rwork0.17214 ---
obs0.17326 35577 99.54 %-
all-39325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0 Å2
2--0.05 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 28 257 1980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191849
X-RAY DIFFRACTIONr_bond_other_d0.0010.021703
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9622506
X-RAY DIFFRACTIONr_angle_other_deg0.78233910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7935226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.11122.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37915308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8351516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9311.159891
X-RAY DIFFRACTIONr_mcbond_other0.9311.156890
X-RAY DIFFRACTIONr_mcangle_it1.5811.7271121
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4311.327958
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 111 -
Rwork0.233 2566 -
obs--99.18 %
Refinement TLS params.Method: refined / Origin x: 12.5785 Å / Origin y: 81.3013 Å / Origin z: 13.9846 Å
111213212223313233
T0.0211 Å20.0038 Å2-0.0169 Å2-0.041 Å2-0.0141 Å2--0.0602 Å2
L0.6032 °2-0.2857 °2-0.0058 °2-1.5021 °20.1762 °2--0.8526 °2
S-0.0442 Å °-0.036 Å °0.0196 Å °0.1722 Å °0.0682 Å °-0.1122 Å °0.0348 Å °-0.0423 Å °-0.024 Å °

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