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- PDB-1p4d: F factor TraI Relaxase Domain -

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Basic information

Entry
Database: PDB / ID: 1p4d
TitleF factor TraI Relaxase Domain
ComponentsTraI protein
KeywordsHYDROLASE / 5-strand antiparallel beta sheet / alpha-beta / 3 histidine Mg(II) coordination
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / metabolic process / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain / Conjugative relaxase, N-terminal / TrwC relaxase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain / Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / AAA domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Multifunctional conjugation protein TraI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsDatta, S. / Larkin, C. / Schildbach, J.F.
Citation
Journal: Structure / Year: 2003
Title: Structural insights into single-stranded DNA binding and cleavage by F factor TraI.
Authors: Datta, S. / Larkin, C. / Schildbach, J.F.
#1: Journal: Biochim.Biophys.Acta / Year: 2003
Title: Subdomain organization and catalytic residues of the F factor TraI relaxase domain
Authors: Street, L.M. / Harley, M.J. / Stern, J.C. / Larkin, C. / Williams, S.L. / Miller, D.L. / Dohm, J.A. / Rodgers, M.E. / Schildbach, J.F.
History
DepositionApr 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: TraI protein
B: TraI protein
C: TraI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,78317
Polymers109,0283
Non-polymers75614
Water2,918162
1
A: TraI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6777
Polymers36,3431
Non-polymers3356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TraI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6777
Polymers36,3431
Non-polymers3356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TraI protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4293
Polymers36,3431
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.219, 128.219, 121.184
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-952-

HOH

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Components

#1: Protein TraI protein / DNA helicase I / Contains: Trai* protein


Mass: 36342.547 Da / Num. of mol.: 3 / Fragment: 36 kDa N-terminal domain of TraI (Residues 1-330)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TRAI / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14565, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 1000, Tris, magnesium chloride, strontium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
pH: 8.25 / Method: vapor diffusion, sitting drop / Details: Larkin, C., (2003) Acta Crystallogr., D59, 1514.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
225 mMTris1droppH8.25
30.1 mMEDTA1drop
40.5 mMbeta-mercaptoethanol1drop
550 mM1dropNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS F210.9713
SYNCHROTRONCHESS F220.9713, 0.9789, 0.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 14, 2003
ADSC QUANTUM 42CCDFeb 14, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double bounce energy tunableSINGLE WAVELENGTHMx-ray1
2double bounce energy tunableMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97131
20.97891
30.97931
ReflectionResolution: 2.6→25 Å / Num. all: 35773 / Num. obs: 34650 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 51.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 43.3
Reflection shellResolution: 2.6→2.76 Å / % possible all: 92.3
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 96.8 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 92.3 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 8.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3441 9.9 %RANDOM
Rwork0.233 ---
all0.238 35773 --
obs0.238 34650 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.1404 Å2 / ksol: 0.364689 e/Å3
Displacement parametersBiso mean: 67.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å25.95 Å20 Å2
2--1.68 Å20 Å2
3----3.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6445 0 47 164 6656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 537 9.9 %
Rwork0.291 4905 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3EGL.PARAMEGL.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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