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- PDB-3gqh: Crystal Structure of the Bacteriophage phi29 gene product 12 C-te... -

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Basic information

Entry
Database: PDB / ID: 3gqh
TitleCrystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment
ComponentsPreneck appendage protein
KeywordsVIRAL PROTEIN / beta barrel
Function / homology
Function and homology information


virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / ATP binding / metal ion binding
Similarity search - Function
Virus Head Decoration Protein; Chain: A, / Head decoration protein D / Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / succinate dehydrogenase protein domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Rhinovirus 14, subunit 4 ...Virus Head Decoration Protein; Chain: A, / Head decoration protein D / Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / succinate dehydrogenase protein domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Rhinovirus 14, subunit 4 / Pectin lyase fold / Pectin lyase fold/virulence factor / Few Secondary Structures / Irregular / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pre-neck appendage protein / Pre-neck appendage protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsXiang, Y. / Rossmann, M.G.
CitationJournal: Mol.Cell / Year: 2009
Title: Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike.
Authors: Xiang, Y. / Leiman, P.G. / Li, L. / Grimes, S. / Anderson, D.L. / Rossmann, M.G.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: Preneck appendage protein
B: Preneck appendage protein
C: Preneck appendage protein


Theoretical massNumber of molelcules
Total (without water)54,0433
Polymers54,0433
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-43 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.144, 84.158, 86.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Preneck appendage protein


Mass: 18014.301 Da / Num. of mol.: 3 / Fragment: D4, Residues 692-854
Source method: isolated from a genetically manipulated source
Details: RESIDUES 692-854 EXPRESSED WITH A N-TERMIINAL HIS6 TAG
Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 12, gene product 12 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: B3VMP8, UniProt: P20345*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE MUTATIONS MIGHT BE AN ACCUMULATED RESULT OF THE PHAGE PASSAGING

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-Tris at pH 7.0, 20% PEG4K and 10% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2008
RadiationMonochromator: SI(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.8→42.08 Å / Num. obs: 55084 / % possible obs: 99.5 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 29.1
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 7 / Num. unique all: 5419 / Rsym value: 0.438 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→42.08 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.642 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2795 5.1 %RANDOM
Rwork0.228 ---
obs0.229 54993 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.66 Å2 / Biso mean: 26.743 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 0 169 3984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223987
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9585398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66124.918183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58615681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7541518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023047
X-RAY DIFFRACTIONr_nbd_refined0.2040.21532
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2207
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.216
X-RAY DIFFRACTIONr_mcbond_it0.9281.52542
X-RAY DIFFRACTIONr_mcangle_it1.55423985
X-RAY DIFFRACTIONr_scbond_it2.05531641
X-RAY DIFFRACTIONr_scangle_it3.2284.51413
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 215 -
Rwork0.233 3785 -
all-4000 -
obs--99.73 %

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