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- PDB-3zmn: VP17, a capsid protein of bacteriophage P23-77 -

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Basic information

Entry
Database: PDB / ID: 3zmn
TitleVP17, a capsid protein of bacteriophage P23-77
Components(VP17) x 2
KeywordsVIRAL PROTEIN
Function / homologyJelly Rolls - #1170 / Immunoglobulin-like - #3410 / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta / VP17
Function and homology information
Biological speciesTHERMUS PHAGE P23-77 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.26 Å
AuthorsRissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.
CitationJournal: Structure / Year: 2013
Title: Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of an Ancient Branch from a Major Virus Lineage.
Authors: Rissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.
History
DepositionFeb 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Atomic model / Database references ...Atomic model / Database references / Non-polymer description / Other / Refinement description
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP17
B: VP17
C: VP17
D: VP17


Theoretical massNumber of molelcules
Total (without water)65,1504
Polymers65,1504
Non-polymers00
Water7,638424
1
A: VP17


Theoretical massNumber of molelcules
Total (without water)31,8761
Polymers31,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VP17


Theoretical massNumber of molelcules
Total (without water)31,8761
Polymers31,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: VP17


  • defined by software
  • 699 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6991
Polymers6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: VP17


  • defined by software
  • 699 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6991
Polymers6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.210, 107.210, 233.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2204-

HOH

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Components

#1: Protein VP17


Mass: 31875.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FOR LOOPS AT 220-225 (CHAIN A) AND 221-226 (CHAIN B), POORLY ORDERED BUT CLEARLY VISIBLE POLYPEPTIDE CHAIN WAS MODELLED AS POLYALANINE.
Source: (gene. exp.) THERMUS PHAGE P23-77 (virus) / Plasmid: PIR1 (ORF17/PET22B) / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: C8CHL5
#2: Protein/peptide VP17


Mass: 698.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHAINS C AND D ARE FRAGMENTS OF THE DISORDERED TERMINI, MODELLED AS UNK.
Source: (gene. exp.) THERMUS PHAGE P23-77 (virus) / Plasmid: PIR1 (ORF17/PET22B) / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): HMS174(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCERTAIN RESIDUES WERE MODELLED WITH TRUNCATED SIDECHAINS. THESE INCLUDE CHAIN A 220-225, CHAIN B ...CERTAIN RESIDUES WERE MODELLED WITH TRUNCATED SIDECHAINS. THESE INCLUDE CHAIN A 220-225, CHAIN B 221-226, AND ENTIRE CHAINS C AND D WHICH ARE FRAGMENTS OF MAINLY DISORDERED TERMINI (RESIDUE NUMBERS AND CHAIN DIRECTION UNKNOWN).

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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: 3.04 Å3/Da / Density % sol: 59.6 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PROTEIN(2-3 MG/ML IN 20 MM TRIS-BUFFER PH 7.4) MIXED 1:1 WITH SOLUTION CONSISTING OF 1.9 M SODIUM FORMATE AND 0.1 M BIS-TRIS BUFFER PH 7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→59.7 Å / Num. obs: 37893 / % possible obs: 100 % / Redundancy: 35.5 % / Biso Wilson estimate: 49.88 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 38.6
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 36.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
xia2data scaling
xia2phasing
SHELXDphasing
autoSHARPphasing
ARP/wARPphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.26→43.94 Å / Cor.coef. Fo:Fc: 0.9393 / Cor.coef. Fo:Fc free: 0.9256 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.158
Details: RESIDUES 1-40 AND 274-291 ARE DISORDERED IN CHAIN A. RESIDUES 1-42 AND 274-291 ARE DISORDERED IN CHAIN B. CHAINS C AND D ARE FRAGMENTS OF THE DISORDERED TERMINI AND MODELLED AS UNK. IT IS ...Details: RESIDUES 1-40 AND 274-291 ARE DISORDERED IN CHAIN A. RESIDUES 1-42 AND 274-291 ARE DISORDERED IN CHAIN B. CHAINS C AND D ARE FRAGMENTS OF THE DISORDERED TERMINI AND MODELLED AS UNK. IT IS UNCLEAR WHICH OF CHAINS (A OR B) THESE POLYPEPTIDE FRAGMENTS BELONG TO.
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1890 5 %RANDOM
Rwork0.1855 ---
obs0.1868 37808 99.38 %-
Displacement parametersBiso mean: 51.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.6185 Å20 Å20 Å2
2--1.6185 Å20 Å2
3----3.2371 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: LAST / Resolution: 2.26→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 0 424 4031
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013717HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.145077HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1209SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes556HARMONIC5
X-RAY DIFFRACTIONt_it3717HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion17.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4080SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2207 142 5.32 %
Rwork0.1875 2528 -
all0.1893 2670 -
obs--99.38 %
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)
11.16330.53830.62840.23440.35010.98720.025-0.00320.0597-0.0398-0.03950.0959-0.0419-0.0480.0144-0.0808-0.0069-0.05460.0376-0.1230.0317-32.036362.905114.7019
22.45310.7461-0.17591.3233-0.39231.7841-0.01920.22370.2561-0.1899-0.08040.0227-0.1121-0.05350.0996-0.0468-0.0003-0.018-0.06790.0005-0.0521-12.551268.24946.8764
33.78920.66790.68170.99980.11430.22610.04180.06710.0376-0.0959-0.11140.0412-0.033-0.08860.0695-0.0503-0.0237-0.04150.0222-0.0938-0.0231-28.465360.875113.5639
40.43381.2450.05721.41890.85240.03610.0577-0.02770.0797-0.0485-0.0527-0.0238-0.1090.0761-0.005-0.0509-0.17990.0090.0141-0.02840.06959.69386.739225.1974
50.626-0.2934-0.80051.56741.05182.3418-0.0163-0.04080.12940.1468-0.09460.1106-0.0569-0.00710.1109-0.0523-0.050.0042-0.0521-0.12040.0334-12.743476.103636.681
62.09071.5929-0.26881.6737-0.20890-0.00370.02160.0559-0.016-0.0178-0.0566-0.10430.12390.0216-0.0937-0.13930.01040.0238-0.05870.05889.888381.681725.6874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 43-94
2X-RAY DIFFRACTION2CHAIN A AND RESID 95-217
3X-RAY DIFFRACTION3CHAIN A AND RESID 218-273
4X-RAY DIFFRACTION4CHAIN B AND RESID 43-98
5X-RAY DIFFRACTION5CHAIN B AND RESID 99-187
6X-RAY DIFFRACTION6CHAIN B AND RESID 188-273

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