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- PDB-4p0y: Structure of the double stranded DNA binding type IV secretion pr... -

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Basic information

Entry
Database: PDB / ID: 4p0y
TitleStructure of the double stranded DNA binding type IV secretion protein TraN from Enterococcus
ComponentsAM32
KeywordsDNA BINDING PROTEIN / GRAM-POSITIVE / CONJUGATION / HELIX-TURN-HELIX / DSDNA BINDING
Function / homologyisomerase activity / AM32
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsGoessweiner-mohr, N. / Fercher, C. / Keller, W.
CitationJournal: 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.
History
DepositionFeb 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AM32
B: AM32


Theoretical massNumber of molelcules
Total (without water)35,5752
Polymers35,5752
Non-polymers00
Water4,161231
1
A: AM32


Theoretical massNumber of molelcules
Total (without water)17,7881
Polymers17,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AM32


Theoretical massNumber of molelcules
Total (without water)17,7881
Polymers17,7881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.100, 62.820, 55.870
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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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: 17787.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: PQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q7BVV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: BIS-TRIS, PEG 3.350, PH 5.5, MICROBATCH UNDER OIL, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2010
Details: TOROIDAL MIRROR (M2) TO VERTICALLY AND HORIZONTALLY FOCUS THE BEAM AT THE SAMPLE POSITION DEMAGNIFICATION)
RadiationMonochromator: BARTELS MONOCROMATOR / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→55.87 Å / Num. obs: 43358 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.085 / Net I/σ(I): 14.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1 / Rsym value: 0.776 / % possible all: 94.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.6.0117refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→21.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.189 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2174 5 %RANDOM
Rwork0.183 ---
obs0.185 41163 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20.2 Å2
2--0.85 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 0 231 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021993
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7011.9612674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48524.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63915396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0171512
X-RAY DIFFRACTIONr_chiral_restr0.1480.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021496
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 133 -
Rwork0.252 2929 -
obs--93.87 %

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