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- PDB-4pm3: Structure of the double-stranded DNA binding type IV secretion pr... -

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Basic information

Entry
Database: PDB / ID: 4pm3
TitleStructure of the double-stranded DNA binding type IV secretion protein TraN from Enterococcus
ComponentsAM32
KeywordsDNA BINDING PROTEIN / Type IV secretion / internal dimer / isomerase
Function / homologyisomerase activity / BROMIDE ION / : / AM32
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
Model detailshelix-turn-helix-like motif, beta-barrel-like motif
AuthorsGoessweiner-Mohr, N. / Keller, W.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2014
Title: Structure of the double-stranded DNA binding type IV secretion protein TraN from Enterococcus
Authors: Goessweiner-Mohr, N. / Eder, M. / Hofer, G. / Fercher, C. / Arends, K. / Birner-Gruenberger, R. / Grohmann, E. / Keller, W.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2012
Title: Crystallization and first data collection of the putative transfer protein TraN from Gram-positive conjugative plasmid pIP501
Authors: Goessweiner-Mohr, N. / Fercher, C. / Abajy, M.Y. / Grohmann, E. / Keller, W.
History
DepositionMay 20, 2014Deposition site: RCSB / Processing site: PDBE
SupersessionJul 30, 2014ID: 4HH7
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AM32
B: AM32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9108
Polymers35,2002
Non-polymers7106
Water4,216234
1
A: AM32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9554
Polymers17,6001
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AM32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9554
Polymers17,6001
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.880, 54.940, 57.710
Angle α, β, γ (deg.)90.00, 91.89, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are two biological units present in the asymmetric unit (chain A, chain B).

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Components

#1: Protein AM32 / Enterococcus faecalis plasmid pAM-beta-1 copy number repressor (copF) / RepE (repE) / resolvase ...Enterococcus faecalis plasmid pAM-beta-1 copy number repressor (copF) / RepE (repE) / resolvase (res beta) / and type I topoisomerase (top beta) genes / Uncharacterized protein


Mass: 17599.949 Da / Num. of mol.: 2 / Fragment: TraN
Source method: isolated from a genetically manipulated source
Details: MKHHHHHHHSDYDIPTTENLYFQGSGS is the 7x N-terminal HisTag HisTag and several N-terminal and C-terminal residues are not visible in the density map.
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BVV5
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.5
Details: 1:1 setup of purification buffer with Index screen condition 42 (0.1 M Bis-Tris, 25.0 % PEG 3350); final protein concentration: 3.25 mg/ml Crystal soaked for 1.5 h with Br4Pt

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Pt LIII high-end remote
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0615 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0615 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Number: 69059 / Rsym value: 0.12 / D res high: 1.8 Å / D res low: 57.679 Å / Num. obs: 19191 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
5.6928.9710.0630.0633.5
4.025.6910.0610.0613.6
3.294.0210.0720.0723.6
2.853.2910.0880.0883.6
2.552.8510.1110.1113.6
2.322.5510.1420.1423.6
2.152.3210.1780.1783.6
2.012.1510.2540.2543.6
1.92.0110.3780.3783.6
1.81.910.5220.5223.6
ReflectionResolution: 1.8→57.68 Å / Num. all: 19191 / Num. obs: 19191 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.79 Å2 / Rpim(I) all: 0.073 / Rrim(I) all: 0.141 / Rsym value: 0.12 / Net I/av σ(I): 4.67 / Net I/σ(I): 8.8 / Num. measured all: 69059
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.93.60.5221.21000428040.3240.5223.7100
1.9-2.013.60.3781.6939226190.2340.3785100
2.01-2.153.60.2542.5891724760.1560.2546.6100
2.15-2.323.60.1783.6837123220.1090.1788.1100
2.32-2.553.60.1424.5771421310.0870.1429.1100
2.55-2.853.60.1115.9694119180.0680.11110.1100
2.85-3.293.60.0886.8624517210.0540.08812.3100
3.29-4.023.60.0727.8522914380.0430.07215.5100
4.02-5.693.60.0618.7406311310.0380.06115.9100
5.69-28.9673.50.0639.121836310.040.06314.999.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation28.97 Å2.01 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
MAR345dtbdata collection
MOSFLM11.0.02data reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P0Z

4p0z


Resolution: 1.8→28.967 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 986 5.14 %
Rwork0.1693 --
obs0.1716 19171 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.8→28.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 6 231 2123
Biso mean--36.93 24.11 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071922
X-RAY DIFFRACTIONf_angle_d0.9622575
X-RAY DIFFRACTIONf_dihedral_angle_d13.216739
X-RAY DIFFRACTIONf_chiral_restr0.042272
X-RAY DIFFRACTIONf_plane_restr0.004331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.89490.25771510.20242583X-RAY DIFFRACTION100
1.8949-2.01360.22951370.18062569X-RAY DIFFRACTION100
2.0136-2.1690.19831410.16262593X-RAY DIFFRACTION100
2.169-2.38720.21851420.16132586X-RAY DIFFRACTION100
2.3872-2.73240.24391440.1822597X-RAY DIFFRACTION100
2.7324-3.44170.21971380.17052595X-RAY DIFFRACTION100
3.4417-28.97060.17891330.15722662X-RAY DIFFRACTION100

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