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- PDB-3suc: Crystal structure of the pre-mature bacteriophage phi29 gene prod... -

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Basic information

Entry
Database: PDB / ID: 3suc
TitleCrystal structure of the pre-mature bacteriophage phi29 gene product 12
ComponentsPreneck appendage protein
KeywordsVIRAL PROTEIN / BETA HELIX / BETA BARREL / ATP BINDING
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 / 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 / Pectate lyase superfamily protein / succinate dehydrogenase protein domain / Parallel beta-helix repeat / Parallel beta-helix repeats ...Insect antifreeze protein / 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 / Pectate lyase superfamily protein / succinate dehydrogenase protein domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Rhinovirus 14, subunit 4 / 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 / 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: 2.15 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. / G Leiman, P. / Li, L. / Grimes, S. / Anderson, D.L. / Rossmann, M.G.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionAug 3, 2011ID: 3GQN
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)83,0025
Polymers82,4061
Non-polymers5964
Water1,31573
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)249,00715
Polymers247,2193
Non-polymers1,78812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area36770 Å2
ΔGint-272 kcal/mol
Surface area67270 Å2
MethodPISA
2
A: Preneck appendage protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)498,01330
Polymers494,4386
Non-polymers3,57524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area74610 Å2
ΔGint-560 kcal/mol
Surface area133470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.889, 95.889, 795.391
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Preneck appendage protein


Mass: 82406.320 Da / Num. of mol.: 1 / Fragment: D1*D2D3D4, RESIDUES 89-854 / Mutation: K166R, K627Q, E695Q, D701G, G817S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Gene: 12 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: B3VMP8, UniProt: P20345*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 4.27 Å3/Da / Density % sol: 71.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.0 M Sodium Acetate at pH 7.0, 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
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 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: 2.15→49.27 Å / Num. obs: 68349 / % possible obs: 88 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 17.143
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6 % / Rmerge(I) obs: 0.446 / % possible all: 57

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3GQ7, 3GQH

3gq7

3gqh


Resolution: 2.15→49.27 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / SU B: 12.931 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2533 5 %RANDOM
Rwork0.261 ---
obs0.262 50808 65.5 %-
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 mean: 48.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å21.11 Å20 Å2
2--2.21 Å20 Å2
3----3.32 Å2
Refinement stepCycle: LAST / Resolution: 2.15→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5746 0 34 73 5853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225905
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.958021
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84524.598261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.915943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5561533
X-RAY DIFFRACTIONr_chiral_restr0.0750.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024513
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.22700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24016
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.2238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5751.53860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94226074
X-RAY DIFFRACTIONr_scbond_it1.54632286
X-RAY DIFFRACTIONr_scangle_it2.44.51942
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 5 -
Rwork0.295 157 -
obs--2.86 %
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)
19.14716.1569-0.57615.6898-0.245236.3394-0.1064-0.53950.36650.4020.01680.0055-0.1122-0.46850.08960.19630.08660.10320.263800.252435.1788-28.7832115.2963
20.7764-0.1149-0.36771.02770.46675.5899-0.0456-0.3721-0.15030.3984-0.03180.15990.6087-0.87890.0774-0.0112-0.16170.06530.1170.04530.056333.5534-37.463475.6968
30.90210.2121-0.0680.4026-0.24414.7220.08650.07360.08470.0093-0.01250.1055-0.2838-0.3448-0.074-0.3780.04180.0053-0.45380.00490.041741.0065-20.479817.2156
43.9066-0.8452-1.6921.07960.95031.8379-0.074-0.0924-0.45320.145-0.09010.02240.4029-0.02360.1642-0.17180.0279-0.0383-0.17250.01340.169549.7157-39.7541-21.3648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 134
2X-RAY DIFFRACTION2A135 - 547
3X-RAY DIFFRACTION3A548 - 681
4X-RAY DIFFRACTION4A682 - 854

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