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- PDB-2q7u: Crystal Structure of the F plasmid TraI Relaxase Domain with the ... -

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Basic information

Entry
Database: PDB / ID: 2q7u
TitleCrystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate
ComponentsProtein traI
KeywordsHYDROLASE / relaxase / conjugation / Alternative initiation / ATP-binding / DNA-binding / Helicase / Nucleotide-binding / Plasmid
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
IMIDO DIPHOSPHATE / THYMIDINE-5'-PHOSPHATE / Multifunctional conjugation protein TraI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLujan, S.A. / Redinbo, M.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase.
Authors: Lujan, S.A. / Guogas, L.M. / Ragonese, H. / Matson, S.W. / Redinbo, M.R.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein traI
B: Protein traI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2265
Polymers66,7052
Non-polymers5213
Water81145
1
A: Protein traI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8744
Polymers33,3521
Non-polymers5213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein traI


Theoretical massNumber of molelcules
Total (without water)33,3521
Polymers33,3521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.500, 86.310, 127.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein traI / DNA helicase I


Mass: 33352.273 Da / Num. of mol.: 2 / Fragment: RELAXASE DOMAIN (UNP residues 1-300) / Mutation: Y16F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: TraI / Gene: traI / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PON / IMIDO DIPHOSPHATE


Mass: 174.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3NO6P2
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein buffer: 50 mM NaCl, 10% glycerol, 10 mM Tris-HCl pH 7.5, mother liquor: 75 mM sodium nitrate, 14% w/v PEG 3350, 10 mM spermine, 110 uM oriT DNA soaked (24 hours): 200 mM ammonium ...Details: protein buffer: 50 mM NaCl, 10% glycerol, 10 mM Tris-HCl pH 7.5, mother liquor: 75 mM sodium nitrate, 14% w/v PEG 3350, 10 mM spermine, 110 uM oriT DNA soaked (24 hours): 200 mM ammonium nitrate, 40% w/v PEG 3350, and 1 mM N,N-imidobisphosphonate (PNP), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97173 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97173 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 11257 / Num. obs: 10447 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.135 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.9 % / Rsym value: 0.382 / % possible all: 72.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREP(CCP4)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1p4d

1p4d


Resolution: 3→38.23 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 116581.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 941 10.4 %RANDOM
Rwork0.214 ---
all0.215 11257 --
obs0.215 9059 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.4911 Å2 / ksol: 0.270574 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.48 Å20 Å20 Å2
2--32.74 Å20 Å2
3----27.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 26 45 4203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.682
X-RAY DIFFRACTIONc_scangle_it4.422.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 125 10.8 %
Rwork0.321 1035 -
obs--68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5pnp.parpnp.top

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