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- PDB-2c5r: The structure of phage phi29 replication organizer protein p16.7 ... -

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Basic information

Entry
Database: PDB / ID: 2c5r
TitleThe structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA
Components
  • 5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3'
  • 5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3'
  • EARLY PROTEIN P16.7
KeywordsDNA-BINDING PROTEIN/DNA / DNA-BINDING PROTEIN-DNA COMPLEX / DNA-BINDING PROTEIN / COMPLEX (DNA-BINDING PROTEIN-DNA)
Function / homology
Function and homology information


viral DNA genome replication / host cell membrane / DNA replication / host cell plasma membrane / DNA binding / membrane
Similarity search - Function
Phage phi29 replication organiser protein p16.7-like / Bacteriophage DNA replication protein Gp16.7 / Bacteriophage DNA replication protein Gp16.7 superfamily / Bacteriophage phi-29 early protein GP16.7 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA replication protein 16.7
Similarity search - Component
Biological speciesBACILLUS PHAGE PHI29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAlbert, A. / Jimenez, M. / Munoz-Espin, D. / Asensio, J.L. / Hermoso, J.A. / Salas, M. / Meijer, W.J.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Basis for Membrane Anchorage of Viral Phi 29 DNA During Replication.
Authors: Albert, A. / Munoz-Espin, D. / Jimenez, M. / Asensio, J.L. / Hermoso, J.A. / Salas, M. / Meijer, W.J.J.
History
DepositionOct 31, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EARLY PROTEIN P16.7
B: EARLY PROTEIN P16.7
C: EARLY PROTEIN P16.7
D: EARLY PROTEIN P16.7
E: EARLY PROTEIN P16.7
F: EARLY PROTEIN P16.7
Y: 5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3'
Z: 5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)52,4838
Polymers52,4838
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.505, 72.111, 127.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A8 - 62
2116B8 - 62
3116C8 - 62
4116D8 - 62
5116E8 - 62
6116F8 - 62

NCS oper:
IDCodeMatrixVector
1given(-0.99855, -0.02281, 0.04882), (-0.02807, -0.5533, -0.83251), (0.04601, -0.83267, 0.55186)39.73845, 27.39048, 13.62338
2given(-0.99826, -0.02638, -0.05282), (0.02369, -0.99842, 0.05092), (-0.05408, 0.04958, 0.9973)34.55003, 32.3389, -0.1936
3given(0.99349, 0.08124, -0.07982), (0.03338, 0.4624, 0.88604), (0.10889, -0.88294, 0.45668)-6.12134, 6.05816, 13.32267
4given(-0.98594, -0.13266, 0.10163), (-0.15831, 0.54668, -0.82224), (0.05352, -0.82677, -0.55999)45.94772, 12.68644, 16.75061
5given(0.99566, 0.04772, 0.07988), (0.05032, 0.44592, -0.89366), (-0.07827, 0.8938, 0.44158)4.79002, 10.35376, -11.41956

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Components

#1: Protein
EARLY PROTEIN P16.7


Mass: 7937.970 Da / Num. of mol.: 6 / Fragment: RESIDUES 64-130
Source method: isolated from a genetically manipulated source
Details: DSDNA AND SSDNA BINDING PROTEIN / Source: (gene. exp.) BACILLUS PHAGE PHI29 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P16517
#2: DNA chain 5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3'


Mass: 2387.581 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3'


Mass: 2467.629 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.2 %

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 12368 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BNK

2bnk


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / SU B: 22.38 / SU ML: 0.418 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 960 7.2 %RANDOM
Rwork0.251 ---
obs0.254 12386 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å20 Å2
2---0.14 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 328 0 51 3535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0213558
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2182.0874874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.95372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1460.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.21598
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4770.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3971.51890
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70723066
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.12831668
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7624.51808
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 459 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.195
2Bloose positional0.215
3Cloose positional0.195
4Dloose positional0.225
5Eloose positional0.215
6Floose positional0.355
1Aloose thermal1.1710
2Bloose thermal1.210
3Cloose thermal1.0210
4Dloose thermal1.0210
5Eloose thermal1.1810
6Floose thermal1.2510
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.394 67
Rwork0.315 864
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)
12.0447-1.2069-0.33634.30771.42672.7576-0.269-0.1114-0.0341-0.05580.12390.050.0022-0.18430.14510.0542-0.05660.10140.34-0.05840.197520.149.702514.2285
279.14423.3714-8.62930.54860.263330.0794-2.1194-0.2171.2836-0.72671.3863-1.3732-0.92130.02550.7331.3280.1334-0.07310.7389-0.02050.747119.924618.044-1.5662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 69
2X-RAY DIFFRACTION1B7 - 69
3X-RAY DIFFRACTION1C7 - 69
4X-RAY DIFFRACTION1D7 - 69
5X-RAY DIFFRACTION1E7 - 69
6X-RAY DIFFRACTION1F7 - 69
7X-RAY DIFFRACTION2Y9 - 16
8X-RAY DIFFRACTION2Z1 - 8

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