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- PDB-1td3: Crystal structure of VSHP_BPP21 in space group C2 -

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Basic information

Entry
Database: PDB / ID: 1td3
TitleCrystal structure of VSHP_BPP21 in space group C2
ComponentsHead decoration protein
KeywordsVIRAL PROTEIN / SHP
Function / homologyVirus Head Decoration Protein; Chain: A, / Head decoration protein D / Head decoration protein D superfamily / Head decoration protein D / Bacteriophage lambda head decoration protein D / viral capsid, decoration / Beta Barrel / Mainly Beta / Head decoration protein
Function and homology information
Biological speciesEnterobacteria phage P21 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsChang, C. / Forrer, P. / Ott, D. / Wlodawer, A. / Plueckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Kinetic Stability and Crystal Structure of the Viral Capsid Protein SHP.
Authors: Forrer, P. / Chang, C. / Ott, D. / Wlodawer, A. / Plueckthun, A.
History
DepositionMay 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2017Group: Structure summary
Revision 1.4Aug 23, 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
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: Head decoration protein
B: Head decoration protein
C: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)35,9653
Polymers35,9653
Non-polymers00
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-12 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.057, 57.724, 62.005
Angle α, β, γ (deg.)90.00, 117.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Head decoration protein / Head protein GPSHP


Mass: 11988.448 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P21 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / Gene: SHP / Production host: Escherichia coli (E. coli) / References: UniProt: P36275
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Na Acetate, PEG-MME 2000, MgSO4, glycine, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.37→60 Å / Num. all: 12968 / Num. obs: 12946 / % possible obs: 99.8 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.37→2.45 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1287 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C5E

1c5e


Resolution: 2.37→44.54 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 320802.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 642 5.2 %RANDOM
Rwork0.206 ---
obs0.206 12465 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.2606 Å2 / ksol: 0.326792 e/Å3
Displacement parametersBiso mean: 43.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å23.57 Å2
2---4.92 Å20 Å2
3---5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-20 Å
Luzzati sigma a0.34 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.37→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 0 387 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.981.5
X-RAY DIFFRACTIONc_mcangle_it3.242
X-RAY DIFFRACTIONc_scbond_it2.512
X-RAY DIFFRACTIONc_scangle_it3.582.5
LS refinement shellResolution: 2.37→2.52 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 102 5.1 %
Rwork0.29 1889 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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