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- PDB-1no4: Crystal Structure of the pre-assembly scaffolding protein gp7 fro... -

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Basic information

Entry
Database: PDB / ID: 1no4
TitleCrystal Structure of the pre-assembly scaffolding protein gp7 from the double-stranded DNA bacteriophage phi29
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 / MAD / Resolution: 2.2 Å
AuthorsMorais, M.C. / Kanamaru, S. / Badasso, M.O. / Koti, J.S. / Owen, B.A.L. / McMurray, C.T. / Anderson, D.L. / 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 15, 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 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Water2,324129
1
A: HEAD MORPHOGENESIS PROTEIN
B: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,3312
Polymers22,3312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-29 kcal/mol
Surface area9800 Å2
MethodPISA
2
C: HEAD MORPHOGENESIS PROTEIN
D: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,3312
Polymers22,3312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-30 kcal/mol
Surface area9450 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-69 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.240, 114.164, 60.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
DetailsThe biological unit is a dimeric coiled-coil. There are two such units 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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 5.56 Å3/Da / Density % sol: 77.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 4 % PEG 8000, 0.16 M calcium acetate, 0.08 M sodium cacodylate, 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: 2.2→60.3 Å / Num. all: 38534 / Num. obs: 38534 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.06 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.068 / Net I/σ(I): 19.5
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 5 / Num. unique all: 1495 / Rsym value: 0.255 / % possible all: 75.4
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 40285 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 75.4 % / Rmerge(I) obs: 0.251

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
XTALVIEWrefinement
SOLVEphasing
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→60.3 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3797 10.1 %RANDOM
Rwork0.239 ---
all0.241 37762 --
obs0.239 37762 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7035 Å2 / ksol: 0.384725 e/Å3
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2---7.99 Å20 Å2
3---9.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→60.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 0 129 2527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 486 9.6 %
Rwork0.324 4571 -
obs--75.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71

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