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

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Basic information

Entry
Database: PDB / ID: 2bnk
TitleThe structure of phage phi29 replication organizer protein p16.7
ComponentsEARLY PROTEIN GP16.7
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
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 replication protein 16.7
Similarity search - Component
Biological speciesBACILLUS PHAGE PHI29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAlbert, A. / Asensio, J.L. / Munoz-Espin, D. / Gonzalez, C. / Hermoso, J.A. / Villar, L. / Jimenez-Barbero, J. / Salas, M. / Meijer, W.J.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of the Functional Domain of {Varphi}29 Replication Organizer: Insights Into Oligomerization and DNA Binding.
Authors: Asensio, J.L. / Albert, A. / Munoz-Espin, D. / Gonzalez, C. / Hermoso, J.A. / Villar, L. / Jimenez-Barbero, J. / Salas, M. / Meijer, W.J.J.
History
DepositionMar 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EARLY PROTEIN GP16.7
B: EARLY PROTEIN GP16.7


Theoretical massNumber of molelcules
Total (without water)15,8762
Polymers15,8762
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.395, 95.395, 47.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.0024, -0.0019), (0.0024, 1, 0.0007), (0.0019, 0.0007, -1)
Vector: 95.4027, -0.1458, 23.7141)

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Components

#1: Protein EARLY PROTEIN GP16.7


Mass: 7937.970 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.94 Å3/Da / Density % sol: 68.75 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 5257 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.3
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.442 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.883 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 281 5.1 %RANDOM
Rwork0.27 ---
obs0.271 5257 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 0 27 1091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9651456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455126
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_restr0.1070.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02804
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.2484
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.5638
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37321038
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8383438
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1244.5418
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: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.397 19
Rwork0.294 388

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