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- PDB-4lu4: Crystal Structure of the N-terminal Fic Domain of a Putative Cell... -

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Basic information

Entry
Database: PDB / ID: 4lu4
TitleCrystal Structure of the N-terminal Fic Domain of a Putative Cell Filamentation protein (VirB-translocated Bep effector protein) 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 / Fic domain / cell filamentation / cell division
Function / homology
Function and homology information


protein adenylyltransferase / regulation of cell division / nucleotidyltransferase activity / nucleotide binding / ATP binding
Similarity search - Function
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
BROMIDE ION / IODIDE ION / protein adenylyltransferase / Putative cell filamentation protein
Similarity search - Component
Biological speciesBartonella quintana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionJul 24, 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 1.2Sep 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
B: Putative cell filamentation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,40916
Polymers52,8632
Non-polymers1,54714
Water5,855325
1
A: Putative cell filamentation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3089
Polymers26,4311
Non-polymers8778
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cell filamentation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1017
Polymers26,4311
Non-polymers6706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.560, 43.630, 88.760
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Putative cell filamentation protein


Mass: 26431.260 Da / Num. of mol.: 2 / Fragment: Fic Domain (unp residues 3-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: JK 31 / Gene: BQ10650 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FYV8, UniProt: A0A0R4I962*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MORPHEUS_b11: 30mM each NaF, NaBr, NaI, 100mM Tris base/Bicine, 15% Glycerol, 15% PEG 4000, pH 8.5, 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 17, 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: 2→50 Å / Num. all: 30189 / Num. obs: 30109 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.18
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.050.3863.13199.9
2.05-2.110.3613.57199.9
2.11-2.170.2954.281100
2.17-2.240.2554.9199.9
2.24-2.310.2195.4199.8
2.31-2.390.1986.05199.9
2.39-2.480.1836.5199.9
2.48-2.580.1627.08199.9
2.58-2.70.1348.1199.8
2.7-2.830.1198.82199.8
2.83-2.980.1089.88199.6
2.98-3.160.09511.06199.8
3.16-3.380.08612.17199.9
3.38-3.650.07513.62199.5
3.65-40.07214.58199.5
4-4.470.06515.22199.4
4.47-5.160.06314.51199.8
5.16-6.320.0713199.6
6.32-8.940.06613.12199.2
8.940.07113.42196.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.92 Å
Translation2.5 Å19.92 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2JK8

2jk8


Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.762 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1993 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23512 1517 5 %RANDOM
Rwork0.18044 ---
obs0.18326 28552 99.64 %-
all-31586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 14 325 3849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193611
X-RAY DIFFRACTIONr_bond_other_d0.0010.023337
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9364880
X-RAY DIFFRACTIONr_angle_other_deg0.92637659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3523.587184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16715599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2291525
X-RAY DIFFRACTIONr_chiral_restr0.10.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
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_it0.9861.0581760
X-RAY DIFFRACTIONr_mcbond_other0.9861.0571759
X-RAY DIFFRACTIONr_mcangle_it1.61.5762197
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5381.2491851
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: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 83 -
Rwork0.221 2115 -
obs--99.82 %
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)
11.1876-0.36090.10481.232-1.09851.9975-0.0787-0.11310.00810.18330.10010.0054-0.0966-0.1295-0.02140.05460.0174-0.00960.0514-0.0240.03446.4538.23170.7437
21.0717-0.46570.13740.8574-0.02460.28210.01380.08160.0552-0.11260.0076-0.04740.0448-0.0017-0.02140.0334-0.00630.01180.03850.00210.030242.128811.7088-15.1563
31.5984-0.9890.7851.9116-0.87492.4341-0.1518-0.2189-0.00540.36640.05470.0377-0.2078-0.21830.09710.08020.0226-0.01170.0909-0.04040.044946.03778.168344.8406
41.0804-0.76250.17251.5625-0.12140.3195-0.03780.03850.0742-0.03430.0334-0.08260.0517-0.01560.00430.039-0.01230.00120.05330.00760.010841.409212.237527.6663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 83
2X-RAY DIFFRACTION2A84 - 219
3X-RAY DIFFRACTION3B7 - 88
4X-RAY DIFFRACTION4B89 - 219

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