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- PDB-1td4: Crystal structure of VSHP_BPP21 in space group H3 with high resol... -

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Basic information

Entry
Database: PDB / ID: 1td4
TitleCrystal structure of VSHP_BPP21 in space group H3 with high resolution.
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)11,9881
Polymers11,9881
Non-polymers00
Water2,990166
1
A: Head decoration protein

A: Head decoration protein

A: Head decoration protein


Theoretical massNumber of molelcules
Total (without water)35,9653
Polymers35,9653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)53.909, 53.909, 77.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

21A-282-

HOH

31A-335-

HOH

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Components

#1: Protein Head decoration protein / Head protein GPSHP


Mass: 11988.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P21 (virus) / Genus: Lambda-like viruses / Species: Enterobacteria phage lambda / Production host: Escherichia coli (E. coli) / References: UniProt: P36275
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.51 Å3/Da / Density % sol: 18.5 %
Crystal growTemperature: 295 K / pH: 4.5
Details: Na Acetate, PEG-MME 5000, MgCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 13405 / % possible obs: 99.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.1
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.4 / % possible all: 98.4

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TD3

1td3


Resolution: 1.5→40 Å / Num. parameters: 8311 / Num. restraintsaints: 8857 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.0326
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 669 5.3 %RANDOM
all0.1377 12731 --
obs0.1261 -94.8 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 912.33
Refinement stepCycle: LAST / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms756 0 0 167 923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0

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