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- PDB-3gq9: Crystal Structure of the Bacteriophage phi29 gene product 12 N-te... -

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Basic information

Entry
Database: PDB / ID: 3gq9
TitleCrystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in an apo form
ComponentsPreneck appendage protein
KeywordsVIRAL PROTEIN / beta helix
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 / symbiont entry into host cell / virion attachment to host cell / ATP binding / metal ion binding
Similarity search - Function
Insect antifreeze protein / Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...Insect antifreeze protein / Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / 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 / Resolution: 2 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 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Preneck appendage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6644
Polymers64,4111
Non-polymers2533
Water6,539363
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)193,99312
Polymers193,2333
Non-polymers7609
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
Buried area27760 Å2
ΔGint-202 kcal/mol
Surface area47380 Å2
MethodPISA
2
A: Preneck appendage protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)387,98524
Polymers386,4656
Non-polymers1,52018
Water1086
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
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area56780 Å2
ΔGint-420 kcal/mol
Surface area93510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.633, 89.633, 585.719
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-858-

HOH

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Components

#1: Protein Preneck appendage protein


Mass: 64410.914 Da / Num. of mol.: 1 / Fragment: D1*D2D3, Residues 89-691
Source method: isolated from a genetically manipulated source
Details: RESIDUES 89-854 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 3.51 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 100mM CHES at ~pH 10.0 and 8% PEG3K. Crystalls obtained were then soaked in a mother liquid containing 10mM EDTA for ~5 hours., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.99 Å
DetectorType: MAR CCD 165 mm / 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: 0.99 Å / Relative weight: 1
ReflectionResolution: 2→43.69 Å / Num. obs: 61778 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.079 / Χ2: 0.944 / Net I/σ(I): 24.302
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.075.90.39760461.186198.7
2.07-2.156.10.31160600.893199
2.15-2.256.40.24260720.924199.3
2.25-2.376.80.20160980.825199.3
2.37-2.527.20.16661350.8199.5
2.52-2.717.60.12361640.834199.6
2.71-2.997.70.09361740.886199.7
2.99-3.427.70.06462030.951199.9
3.42-4.317.50.04563101.087199.9
4.31-5070.03965161.081199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2→43.69 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.745 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3077 5 %RANDOM
Rwork0.172 ---
obs0.174 61145 98.47 %-
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: 57.16 Å2 / Biso mean: 23.137 Å2 / Biso min: 10.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 15 363 4856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214655
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9416338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7755634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27324.439205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08815739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7191528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023586
X-RAY DIFFRACTIONr_nbd_refined0.2050.22190
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2361
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.242
X-RAY DIFFRACTIONr_mcbond_it0.4931.53011
X-RAY DIFFRACTIONr_mcangle_it0.96724851
X-RAY DIFFRACTIONr_scbond_it1.81631681
X-RAY DIFFRACTIONr_scangle_it2.9754.51471
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 212 -
Rwork0.22 4149 -
all-4361 -
obs--97.11 %

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