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

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Basic information

Entry
Database: PDB / ID: 3gqa
TitleCrystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with cobalt ions
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 / 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 / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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 / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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
: / PHOSPHATE ION / Pre-neck appendage protein / Pre-neck appendage protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.4Sep 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 / pdbx_struct_conn_angle / 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 / _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)64,6244
Polymers64,4111
Non-polymers2133
Water3,963220
1
A: Preneck appendage protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)387,74324
Polymers386,4656
Non-polymers1,27718
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 area56160 Å2
ΔGint-482 kcal/mol
Surface area93080 Å2
MethodPISA
2
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)193,87112
Polymers193,2333
Non-polymers6399
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 area27550 Å2
ΔGint-233 kcal/mol
Surface area47070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.741, 89.741, 584.795
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-766-

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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 100mM Tris-base at pH 10.5 and 8% PEG3K. Apo crystals were obtained by soaking the crystals in a mother liquid containing 10mM EDTA. The cobalt derivative was obtained by back soaking the ...Details: 100mM Tris-base at pH 10.5 and 8% PEG3K. Apo crystals were obtained by soaking the crystals in a mother liquid containing 10mM EDTA. The cobalt derivative was obtained by back soaking the apo-crystals in a mother liquid containing 10mM cobalt ions, 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: 2.1→43.88 Å / Num. obs: 53528 / % possible obs: 99.5 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.099 / Χ2: 1.843 / Net I/σ(I): 31.667
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.188.70.55552791.3081100
2.18-2.268.70.40552851.4251100
2.26-2.378.70.34953261.4571100
2.37-2.498.70.29353181.4791100
2.49-2.658.70.22353051.613199.9
2.65-2.858.60.16553071.789199.8
2.85-3.148.60.11453561.98199.3
3.14-3.598.40.0853662.425199.1
3.59-4.528.10.05753602.705198.8
4.52-5080.04656262.34198.6

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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: 3GQ7

3gq7


Resolution: 2.1→43.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.317 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2708 5.1 %RANDOM
Rwork0.18 ---
obs0.182 53508 99.49 %-
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: 74.63 Å2 / Biso mean: 29.128 Å2 / Biso min: 16.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20.92 Å20 Å2
2--1.83 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 7 220 4700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214571
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9396209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9965611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90724.45200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2915715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7831527
X-RAY DIFFRACTIONr_chiral_restr0.0980.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023508
X-RAY DIFFRACTIONr_nbd_refined0.2110.22070
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.2149
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.232
X-RAY DIFFRACTIONr_mcbond_it0.6911.53058
X-RAY DIFFRACTIONr_mcangle_it1.12124774
X-RAY DIFFRACTIONr_scbond_it2.05831711
X-RAY DIFFRACTIONr_scangle_it3.1744.51431
LS refinement shellResolution: 2.1→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 201 -
Rwork0.229 3691 -
all-3892 -
obs--99.92 %

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