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

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Basic information

Entry
Database: PDB / ID: 3gqk
TitleCrystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment in complex with ATP
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
ADENOSINE-5'-TRIPHOSPHATE / Pre-neck appendage protein / Pre-neck appendage protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Advisory / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Preneck appendage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5463
Polymers18,0141
Non-polymers5312
Water543
1
A: Preneck appendage protein
hetero molecules

A: Preneck appendage protein
hetero molecules

A: Preneck appendage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6379
Polymers54,0433
Non-polymers1,5946
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8110 Å2
ΔGint-62 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.211, 85.211, 85.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Preneck appendage protein


Mass: 18014.301 Da / Num. of mol.: 1 / 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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-Tris at pH 7.0, 20% PEG4K, 10%v/v MPD, 10mM MgCl2 and 10mM ATP, 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: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→26.95 Å / Num. obs: 7288 / % possible obs: 98.6 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.042 / Χ2: 1.35 / Net I/σ(I): 56.473
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5911.10.557301.4461100
2.59-2.6911.10.3287311.5011100
2.69-2.8211.10.2167151.531100
2.82-2.9611.10.1427211.5581100
2.96-3.1511.10.0937351.5331100
3.15-3.3911.10.0597241.1661100
3.39-3.73110.0437541.0291100
3.73-4.2710.60.0447341.402199.9
4.27-5.3810.60.0357451.0241100
5.38-509.50.0246991.305187.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GQH

3gqh


Resolution: 2.5→26.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.88 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 30.871 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.596 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.334 334 4.6 %RANDOM
Rwork0.264 ---
obs0.267 7244 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.6 Å2 / Biso mean: 43.909 Å2 / Biso min: 26.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 32 3 1309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221332
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9911808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4595162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0542560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46115226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.56156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02997
X-RAY DIFFRACTIONr_nbd_refined0.2310.2562
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.27
X-RAY DIFFRACTIONr_mcbond_it0.6871.5826
X-RAY DIFFRACTIONr_mcangle_it1.17121294
X-RAY DIFFRACTIONr_scbond_it1.8273584
X-RAY DIFFRACTIONr_scangle_it2.9984.5514
LS refinement shellResolution: 2.5→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.517 27 -
Rwork0.409 497 -
all-524 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.4042-0.4503-1.53619.051-1.4647.98650.4177-0.00361.73410.77390.0597-0.0182-1.7669-0.01-0.47740.48760.01670.1070.01790.01260.461-0.746519.071.8037
24.63883.5675-1.34566.1614-5.0295.05810.28540.55220.5995-0.66430.36021.42510.6792-0.9961-0.64560.61870.03020.06740.7680.18510.7068-20.0481-7.524411.7136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A692 - 741
2X-RAY DIFFRACTION1A789 - 854
3X-RAY DIFFRACTION2A742 - 788

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