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- PDB-4jf8: Crystal structure of a TrwG component of type IV secretion system... -

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Basic information

Entry
Database: PDB / ID: 4jf8
TitleCrystal structure of a TrwG component of type IV secretion system protein from Bartonella birtlesii
ComponentsTrwG component of type IV secretion system
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / cat scratch fever / secretion / host specific adhesion
Function / homology
Function and homology information


protein secretion by the type IV secretion system / endomembrane system / membrane
Similarity search - Function
VirB8 protein / Type IV secretion system protein VirB8/PtlE / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Type IV secretion system protein virB8
Similarity search - Component
Biological speciesBartonella birtlesii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: MBio / Year: 2015
Title: Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems.
Authors: Gillespie, J.J. / Phan, I.Q. / Scheib, H. / Subramanian, S. / Edwards, T.E. / Lehman, S.S. / Piitulainen, H. / Rahman, M.S. / Rennoll-Bankert, K.E. / Staker, B.L. / Taira, S. / Stacy, R. / ...Authors: Gillespie, J.J. / Phan, I.Q. / Scheib, H. / Subramanian, S. / Edwards, T.E. / Lehman, S.S. / Piitulainen, H. / Rahman, M.S. / Rennoll-Bankert, K.E. / Staker, B.L. / Taira, S. / Stacy, R. / Myler, P.J. / Azad, A.F. / Pulliainen, A.T.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TrwG component of type IV secretion system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5935
Polymers20,3451
Non-polymers2484
Water4,125229
1
A: TrwG component of type IV secretion system
hetero molecules

A: TrwG component of type IV secretion system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,18610
Polymers40,6892
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1370 Å2
ΔGint-14 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.150, 72.150, 47.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

21A-608-

HOH

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Components

#1: Protein TrwG component of type IV secretion system


Mass: 20344.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella birtlesii (bacteria) / Gene: trwG / Production host: Escherichia coli (E. coli) / References: UniProt: D0AAZ5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.75 Å3/Da / Density % sol: 29.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BabiA.18388.a.B2 PS01693 at 25.7 mg/mL against JCSG+ screen condition A3, 0.2 M citrate, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, unique puck ID vff2-9, crystal tracking ID ...Details: BabiA.18388.a.B2 PS01693 at 25.7 mg/mL against JCSG+ screen condition A3, 0.2 M citrate, 25% PEG 3350 with 20% ethylene glycol as cryo-protectant, unique puck ID vff2-9, crystal tracking ID 240866a3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 31634 / Num. obs: 31529 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 34.59
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.35-1.390.4972.9198.6
1.39-1.420.4583.81198.9
1.42-1.460.385.691100
1.46-1.510.3057.551100
1.51-1.560.2359.941100
1.56-1.610.18912.251100
1.61-1.670.1515.341100
1.67-1.740.1218.95199.9
1.74-1.820.09523.771100
1.82-1.910.0731.061100
1.91-2.010.04942.121100
2.01-2.130.03752.731100
2.13-2.280.03262.21100
2.28-2.460.02770.23199.9
2.46-2.70.02576.141100
2.7-3.020.02483.991100
3.02-3.490.01899.711100
3.49-4.270.015112.051100
4.27-6.040.014111.21199.3
6.040.015103.74190

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.07 Å
Translation3 Å19.07 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bhm

2bhm


Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.555 / SU ML: 0.033 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17514 1588 5 %RANDOM
Rwork0.15426 ---
obs0.15528 29908 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.2 Å20 Å2
2---0.39 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1134 0 16 229 1379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021242
X-RAY DIFFRACTIONr_bond_other_d0.0010.021159
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9451703
X-RAY DIFFRACTIONr_angle_other_deg0.72732648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20223.84665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98815199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6811511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
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_it0.8141.052597
X-RAY DIFFRACTIONr_mcbond_other0.8011.05596
X-RAY DIFFRACTIONr_mcangle_it1.3531.574750
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2071.191645
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_restr1.76932448
X-RAY DIFFRACTIONr_sphericity_free26.635537
X-RAY DIFFRACTIONr_sphericity_bonded6.7352621
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 107 -
Rwork0.213 2161 -
obs--98.05 %
Refinement TLS params.Method: refined / Origin x: 2.4272 Å / Origin y: 24.1056 Å / Origin z: -7.391 Å
111213212223313233
T0.0136 Å2-0.0039 Å2-0.005 Å2-0.0038 Å20.0007 Å2--0.0165 Å2
L0.2805 °20.0375 °20.0843 °2-0.2567 °20.1184 °2--0.3053 °2
S-0.0028 Å °-0.0194 Å °0.0207 Å °-0.0468 Å °0.007 Å °0.0096 Å °0.013 Å °-0.0177 Å °-0.0042 Å °

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