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- PDB-4hic: Crystal structure of the potential transfer protein TraK from Gra... -

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Basic information

Entry
Database: PDB / ID: 4hic
TitleCrystal structure of the potential transfer protein TraK from Gram-positive conjugative plasmid pIP501
ComponentsTraK
KeywordsUNKNOWN FUNCTION / Gram-positive / type-IV secretion / pIP501 / anti-parallel beta-sheets
Function / homology: / Potential transfer protein TraK / membrane / Sigma
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.001 Å
AuthorsGoessweiner-Mohr, N. / Keller, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The type IV secretion protein TraK from the Enterococcus conjugative plasmid pIP501 exhibits a novel fold
Authors: Goessweiner-Mohr, N. / Fercher, C. / Arends, K. / Birner-Gruenberger, R. / Laverde-Gomez, D. / Huebner, J. / Grohmann, E. / Keller, W.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TraK
B: TraK


Theoretical massNumber of molelcules
Total (without water)61,2872
Polymers61,2872
Non-polymers00
Water00
1
A: TraK


Theoretical massNumber of molelcules
Total (without water)30,6441
Polymers30,6441
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TraK


Theoretical massNumber of molelcules
Total (without water)30,6441
Polymers30,6441
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.040, 114.040, 120.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein TraK


Mass: 30643.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: ORF11 from conjugative plasmid pIP501 / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8L1C9

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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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion: microbatch under oil / pH: 6.5
Details: 1:1 setup of purification buffer with Morpheus screen condition 52 (12.5 % PEG 1000, 12.5 % PEG 3350, 12.5 % MPD, ethylene glycols mix, 0.1 M MES/Imidazol); final protein concentration: 6.45 ...Details: 1:1 setup of purification buffer with Morpheus screen condition 52 (12.5 % PEG 1000, 12.5 % PEG 3350, 12.5 % MPD, ethylene glycols mix, 0.1 M MES/Imidazol); final protein concentration: 6.45 mg/ml, pH 6.5, vapor diffusion: microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2010
Details: toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification)
RadiationMonochromator: BARTELS MONOCROMATOR / Protocol: Native / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -h,k,-l / Fraction: 0.24
ReflectionResolution: 3.001→82.835 Å / Num. all: 15465 / Num. obs: 15465 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.094 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.167.60.8320.91693322310.832100
3.16-3.357.60.4781.61634921490.478100
3.35-3.597.60.2982.51524019990.298100
3.59-3.877.60.1754.31418918620.175100
3.87-4.247.60.1444.61294717130.144100
4.24-4.747.60.0759.61189715580.075100
4.74-5.487.60.06610.61040613650.066100
5.48-6.717.60.1076.1901611870.107100
6.71-9.497.50.05312.468079030.053100
9.49-40.3197.20.02922.835814980.02998.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å40.32 Å
Translation3.5 Å40.32 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
PHENIXdev_1088refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.001→40.319 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7381 / σ(F): 0 / Phase error: 33.08 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 770 4.98 %Random
Rwork0.205 ---
all0.2128 15465 --
obs0.2128 15465 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.11 Å2 / Biso mean: 59.7934 Å2 / Biso min: 32.07 Å2
Refinement stepCycle: LAST / Resolution: 3.001→40.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 0 0 3310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113382
X-RAY DIFFRACTIONf_angle_d1.5774566
X-RAY DIFFRACTIONf_chiral_restr0.093488
X-RAY DIFFRACTIONf_plane_restr0.006588
X-RAY DIFFRACTIONf_dihedral_angle_d16.9021228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.0017-3.23330.39011480.35829173065
3.2333-3.55820.30391610.276429083069
3.5582-4.07210.27191450.239329383083
4.0721-5.12660.22111600.193829243084
5.1266-30.94620.19441560.168129843140

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