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- PDB-1yq5: PRD1 vertex protein P5 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1yq5
TitlePRD1 vertex protein P5
ComponentsMinor capsid protein
KeywordsVIRAL PROTEIN / beta-spiral / beta-jelly-roll
Function / homology
Function and homology information


icosahedral viral capsid, spike
Similarity search - Function
Minor capsid protein. / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5 C-terminal domain superfamily / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P5, spike N-terminal / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage PRD1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMerckel, M.C. / Huiskonen, J.T. / Goldman, A. / Bamford, D.H. / Tuma, R.
CitationJournal: Mol.Cell / Year: 2005
Title: The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture.
Authors: Merckel, M.C. / Huiskonen, J.T. / Bamford, D.H. / Goldman, A. / Tuma, R.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor capsid protein
B: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)29,1892
Polymers29,1892
Non-polymers00
Water4,143230
1
A: Minor capsid protein

A: Minor capsid protein

A: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)43,7833
Polymers43,7833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5630 Å2
ΔGint-44 kcal/mol
Surface area14380 Å2
MethodPISA, PQS
2
B: Minor capsid protein

B: Minor capsid protein

B: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)43,7833
Polymers43,7833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area5580 Å2
ΔGint-45 kcal/mol
Surface area14410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.370, 114.370, 114.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe biological assembly is a trimer generated from the chain A in the asymmetric unit by the operations: z,x,y and y,z,x.

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Components

#1: Protein Minor capsid protein / PRD1 vertex protein P5 / Protein P5


Mass: 14594.293 Da / Num. of mol.: 2 / Fragment: residues 197-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage PRD1 (virus) / Genus: Tectivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P22536
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na-formate, Na-acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978335, 0.978497, 0.885595
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 1, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9783351
20.9784971
30.8855951
ReflectionResolution: 2→20 Å / Num. all: 33901 / Num. obs: 33901 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→19.91 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 3338 Random
Rwork0.217 --
obs0.217 33503 -
all-33503 -
Refinement stepCycle: LAST / Resolution: 2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 230 2260
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2

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