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- PDB-3zn4: VP16, a capsid protein of bacteriophage P23-77 (VP16-type-2) -

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Basic information

Entry
Database: PDB / ID: 3zn4
TitleVP16, a capsid protein of bacteriophage P23-77 (VP16-type-2)
ComponentsVP16
KeywordsVIRAL PROTEIN
Function / homologyJelly Rolls - #1180 / : / Major capsid protein VP16-like / Jelly Rolls / Sandwich / Mainly Beta / identical protein binding / CITRIC ACID / VP16
Function and homology information
Biological speciesTHERMUS PHAGE P23-77 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3553
Polymers19,1281
Non-polymers2282
Water4,594255
1
A: VP16
hetero molecules

A: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7116
Polymers38,2562
Non-polymers4554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5580 Å2
ΔGint-59.2 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.600, 68.570, 31.580
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-122-

LEU

21A-1169-

CL

31A-2040-

HOH

41A-2054-

HOH

51A-2055-

HOH

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Components

#1: Protein VP16


Mass: 19127.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SUBUNIT OF A STRAND-SWAPPED HOMODIMER / Source: (gene. exp.) THERMUS PHAGE P23-77 (virus) / Plasmid: PIR2 (ORF16/PET22B) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: C8CHL4
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.15 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4
Details: SITTING DROP VAPOUR DIFFUSION SYSTEM IN A 96-WELL PLATE, 200 NL OF PROTEIN (2-3 MG/ML IN 20 MM TRIS-BUFFER PH 7.4) MIXED WITH 200 NL SOLUTION CONSISTING 20%(W/V) PEG6000 AND 0.1 M CITRATE PH 4.

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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: 1.26→34.3 Å / Num. obs: 37146 / % possible obs: 85.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 10.67 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.1
Reflection shellResolution: 1.26→1.3 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.6 / % possible all: 41.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZMO

3zmo


Resolution: 1.26→17.79 Å / Cor.coef. Fo:Fc: 0.9655 / Cor.coef. Fo:Fc free: 0.9548 / SU R Cruickshank DPI: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.049 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.049
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. RESIDUES 1-18 AND 168-173 ARE ALTERNATE CONFORMATIONS WERE MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1855 5 %RANDOM
Rwork0.1563 ---
obs0.1577 37133 84.96 %-
Displacement parametersBiso mean: 16.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.1331 Å20 Å2-0.983 Å2
2--0.3885 Å20 Å2
3---0.7446 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.26→17.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 14 255 1436
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011293HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.081779HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d434SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes193HARMONIC5
X-RAY DIFFRACTIONt_it1293HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.41
X-RAY DIFFRACTIONt_other_torsion12.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion162SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies10HARMONIC1
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1727SEMIHARMONIC4
LS refinement shellResolution: 1.26→1.29 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2191 70 5.7 %
Rwork0.2001 1158 -
all0.2012 1228 -
obs--84.96 %
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)
12.98140.1664-0.75340.2263-0.06310.5287-0.038-0.13640.10590.01760.0350.01190.01190.02480.003-0.00480.00140.0068-0.00620.0013-0.0128-9.3275-14.95334.1585
20.14460.1030.12130.3005-0.11560.40920.00790.00030.02210.0327-0.0133-0.01340.06590.03980.0054-0.0013-0.0040.0141-0.0083-0.0024-0.001116.467-19.06280.8917
30.92570.61920.57131.22381.28491.4926-0.00270.02930.00530.025-0.00060.0186-0.007-0.06190.00330.00420.00090.0088-0.00730.0101-0.01955.4427-22.18430.2896
41.65150.10960.56971.32410.3611.62750.0013-0.0326-0.02450.06180.0498-0.05140.06160.1737-0.051-0.02450.00850.0104-0.00850.002-0.031516.9725-22.317311.2609
50.01610.2652-0.07350.03580.08020.03610.0001-0.0094-0.0058-0.00060.00590.0115-0.0054-0.0035-0.0060.05050.02010.0306-0.0199-0.0019-0.00058.9855-39.15087.3228
60.66570.33060.00010.8106-0.10440.525-0.0037-0.01010.0349-0.045-0.0121-0.0062-0.00550.01950.0157-0.00850.00160.0099-0.01010-0.016714.4616-17.4275-0.579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|19 - A|39 }
2X-RAY DIFFRACTION2{ A|40 - A|69 }
3X-RAY DIFFRACTION3{ A|70 - A|94 }
4X-RAY DIFFRACTION4{ A|95 - A|123 }
5X-RAY DIFFRACTION5{ A|124 - A|129 }
6X-RAY DIFFRACTION6{ A|130 - A|167 }

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