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- PDB-1noh: The structure of bacteriophage phi29 scaffolding protein gp7 afte... -

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Basic information

Entry
Database: PDB / ID: 1noh
TitleThe structure of bacteriophage phi29 scaffolding protein gp7 after prohead assembly
ComponentsHEAD MORPHOGENESIS PROTEIN
KeywordsVIRAL PROTEIN / coiled-coil
Function / homology
Function and homology information


viral scaffold / virion assembly / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Capsid assembly scaffolding protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMorais, M.C. / Kanamaru, S. / Badasso, M.O. / Koti, J.S. / Owen, B.L. / McMurray, C.T. / L Anderson, D. / Rossmann, M.G.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Bacteriophage f29 scaffolding protein gp7 before and after prohead assembly
Authors: Morais, M.C. / Kanamaru, S. / Badasso, M.O. / Koti, J.S. / Owen, B.A.L. / McMurray, C.T. / Anderson, D.L. / Rossmann, M.G.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAD MORPHOGENESIS PROTEIN
B: HEAD MORPHOGENESIS PROTEIN
C: HEAD MORPHOGENESIS PROTEIN
D: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,6614
Polymers44,6614
Non-polymers00
Water00
1
A: HEAD MORPHOGENESIS PROTEIN
B: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,3312
Polymers22,3312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-28 kcal/mol
Surface area9510 Å2
MethodPISA
2
C: HEAD MORPHOGENESIS PROTEIN
D: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,3312
Polymers22,3312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-27 kcal/mol
Surface area9350 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-65 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.005, 117.301, 105.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsThe biological unit is a dimeric coiled-coil. There are two such dimers per asymmetric unit.

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Components

#1: Protein
HEAD MORPHOGENESIS PROTEIN / Bacteriophage phi29 scaffolding protein gp7 / LATE PROTEIN GP7 / gene 7 protein'


Mass: 11165.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: gp7 / Plasmid: pARgp7 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P13848

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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: 5.37 Å3/Da / Density % sol: 76.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14.4 % Peg 8000, 0.08 M sodium cacodylate, 0.16 M calcium acetate, 20 % glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114.4 %(v/v)PEG800011
20.08 Msodium cacodylate11pH6.5
30.16 Mcadmium acetate11
420 %(v/v)glycerol11
51 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→36.15 Å / Num. all: 27757 / Num. obs: 27757 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.091 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.4 / Num. unique all: 1568 / Rsym value: 0.473 / % possible all: 95.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 17904 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.473

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NO4

1no4


Resolution: 2.8→36.15 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2582 9.3 %RANDOM
Rwork0.254 ---
all0.258 27757 --
obs0.254 27757 82.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9522 Å2 / ksol: 0.344448 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å20 Å2
2---11.24 Å20 Å2
3---14.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 2.8→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 0 0 2356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 368 10.1 %
Rwork0.402 3276 -
obs--65 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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