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- PDB-1td0: Viral capsid protein SHP at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 1td0
TitleViral capsid protein SHP at pH 5.5
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: 1.95 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 14, 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

Downloads & links

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Assembly

Deposited unit
A: Head decoration protein
B: Head decoration protein
C: Head decoration protein
D: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)47,4294
Polymers47,4294
Non-polymers00
Water11,259625
1
A: Head decoration protein

A: Head decoration protein

A: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)35,5723
Polymers35,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
B: Head decoration protein

B: Head decoration protein

B: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)35,5723
Polymers35,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
3
C: Head decoration protein

C: Head decoration protein

C: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)35,5723
Polymers35,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
4
D: Head decoration protein

D: Head decoration protein

D: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)35,5723
Polymers35,5723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Unit cell
Length a, b, c (Å)57.482, 57.482, 101.608
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Head decoration protein / Head protein GPSHP / SHP


Mass: 11857.251 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage P21 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / References: UniProt: P36275
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: sodium Acetate, PEG 5000 MME, MgCl2, pH 5.5, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 27034 / Num. obs: 27034 / % possible obs: 98.5 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2670 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.74 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 593042.35 / 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
Rfree0.26 1283 4.9 %RANDOM
Rwork0.229 ---
obs0.229 26376 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 105.097 Å2 / ksol: 0.326935 e/Å3
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å22.74 Å20 Å2
2--2.55 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-20 Å
Luzzati sigma a0.35 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 0 625 3536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it2.812
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.152.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 201 4.9 %
Rwork0.327 3913 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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