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- PDB-2nra: Crystal structure of Pi initiator protein in complex with iteron DNA -

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Basic information

Entry
Database: PDB / ID: 2nra
TitleCrystal structure of Pi initiator protein in complex with iteron DNA
Components
  • 5'-D(*GP*AP*AP*CP*AP*TP*GP*AP*GP*AP*GP*CP*TP*TP*AP*GP*TP*AP*CP*GP*TP*CP*T)-3'
  • 5'-D(*GP*AP*CP*GP*TP*AP*CP*TP*AP*AP*GP*CP*TP*CP*TP*CP*AP*TP*GP*TP*TP*CP*T)-3'
  • PI protein
KeywordsREPLICATION/DNA / PROTEIN-DNA COMPLEX / DNA REPLICATION / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA replication initiation / DNA-directed DNA polymerase activity
Similarity search - Function
Initiator Rep protein / Initiator Replication protein, WH1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / PI protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsSwan, M.K. / Bastia, D. / Davies, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication.
Authors: Swan, M.K. / Bastia, D. / Davies, C.
History
DepositionNov 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*AP*AP*CP*AP*TP*GP*AP*GP*AP*GP*CP*TP*TP*AP*GP*TP*AP*CP*GP*TP*CP*T)-3'
B: 5'-D(*GP*AP*CP*GP*TP*AP*CP*TP*AP*AP*GP*CP*TP*CP*TP*CP*AP*TP*GP*TP*TP*CP*T)-3'
C: PI protein


Theoretical massNumber of molelcules
Total (without water)45,9353
Polymers45,9353
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.900, 125.900, 138.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain 5'-D(*GP*AP*AP*CP*AP*TP*GP*AP*GP*AP*GP*CP*TP*TP*AP*GP*TP*AP*CP*GP*TP*CP*T)-3'


Mass: 7104.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Iteron oligonucleotide
#2: DNA chain 5'-D(*GP*AP*CP*GP*TP*AP*CP*TP*AP*AP*GP*CP*TP*CP*TP*CP*AP*TP*GP*TP*TP*CP*T)-3'


Mass: 7006.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Iteron oligonucleotide
#3: Protein PI protein / Replication initiation protein


Mass: 31823.906 Da / Num. of mol.: 1 / Mutation: P42L, P106L, F107S, P113S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pir / Plasmid: pTXB1-intein / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P03067

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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: 3.4 Å3/Da / Density % sol: 63.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5% polyethylene glycol 8000, 50 mM MgCl2 and 100 mM NH4H2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1polyethylene glycol 800011
2MgCl211
3NH4H2PO411
4H2O11
5polyethylene glycol 800012
6MgCl212
7NH4H2PO412
8H2O12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11.076
SYNCHROTRONNSLS X12B20.9201, 0.9208, 0.9184
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 23, 2005
ADSC QUANTUM 3152CCDMay 8, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si-220SINGLE WAVELENGTHMx-ray1
2Si-111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0761
20.92011
30.92081
40.91841
ReflectionResolution: 3.1→35.1 Å / Num. all: 12173 / Num. obs: 12173 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 106.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 44.9
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1193 / Rsym value: 0.449 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→35.1 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / SU B: 42.311 / SU ML: 0.355 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The single wavelength data were used for refinement. The MAD data were used to solve the initial structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 593 4.9 %RANDOM
Rwork0.224 ---
all0.227 12161 --
obs0.227 12161 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 3.1→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 936 0 0 2936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223083
X-RAY DIFFRACTIONr_angle_refined_deg1.8542.3614355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7085250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86623.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.67215384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8681512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021951
X-RAY DIFFRACTIONr_nbd_refined0.2540.21366
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3490.25
X-RAY DIFFRACTIONr_mcbond_it0.6781.51282
X-RAY DIFFRACTIONr_mcangle_it1.19922013
X-RAY DIFFRACTIONr_scbond_it1.2932310
X-RAY DIFFRACTIONr_scangle_it2.1934.52342
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 46 -
Rwork0.257 836 -
obs-882 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.84161.48-0.26675.029-0.78733.7299-0.0475-0.210.0690.06770.364-0.2343-0.1722-0.0651-0.31650.06530.01680.08910.0367-0.1892-0.0933-14.61995.93544.338
23.05810.63582.20633.4176-0.75975.2962-0.42220.16690.296-0.44950.65120.2544-0.5293-0.0264-0.2290.0666-0.04090.1350.0403-0.0471-0.151-21.497101.49633.659
30.65860.63330.58231.46741.43191.40070.2570.2475-0.3114-0.79340.30780.08930.91410.1829-0.56490.4555-0.0897-0.09580.5260.09220.0045-26.52181.57926.446
40.31330.59990.61991.80061.95272.1260.13180.2926-0.4157-0.66920.40760.32650.43790.1679-0.53940.4062-0.1998-0.0730.3660.0856-0.0091-27.7785.23421.639
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CC9 - 1049 - 104
2X-RAY DIFFRACTION2CC113 - 268113 - 268
3X-RAY DIFFRACTION3AA2 - 232 - 23
4X-RAY DIFFRACTION4BB25 - 462 - 23

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