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- PDB-4zjn: Crystal structure of the bacteriophage G20C portal protein -

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Basic information

Entry
Database: PDB / ID: 4zjn
TitleCrystal structure of the bacteriophage G20C portal protein
ComponentsPortal protein
KeywordsTRANSPORT PROTEIN / bacteriophage portal protein
Function / homology: / Phage P23-45 portal protein / Portal protein
Function and homology information
Biological speciesBacteriophage G20C (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsWilliams, L.S. / Turkenburg, J.P. / Levdikov, V.M. / Minakhin, L. / Severinov, K. / Antson, A.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
CitationJournal: To be published
Title: Crystal structure of the bacteriophage G20C portal protein
Authors: Williams, L.S. / Turkenburg, J.P. / Levdikov, V.M. / Minakhin, L. / Severinov, K. / Antson, A.A.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9976
Polymers141,6423
Non-polymers3553
Water8,017445
1
A: Portal protein
B: Portal protein
C: Portal protein
hetero molecules

A: Portal protein
B: Portal protein
C: Portal protein
hetero molecules

A: Portal protein
B: Portal protein
C: Portal protein
hetero molecules

A: Portal protein
B: Portal protein
C: Portal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,98724
Polymers566,56912
Non-polymers1,41812
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area136060 Å2
ΔGint-921 kcal/mol
Surface area167100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.328, 155.328, 115.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Portal protein


Mass: 47214.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage G20C (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXR3
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein in 1 M NaCl, 10 mM HEPES pH 7.5. Reservoir: 0.2 M magnesium chloride, 40%(v/v) MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→44.4 Å / Num. all: 98102 / Num. obs: 97710 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.3
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 4815 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimlessdata scaling
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→44.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.531 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.205 977 1 %RANDOM
Rwork0.17465 ---
obs0.17496 96716 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.98→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9619 0 24 445 10088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199901
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9713444
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92751232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72124.229428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.877151700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.11557
X-RAY DIFFRACTIONr_chiral_restr0.0970.21529
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217417
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2072.7744931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.874.6686159
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9813.1374970
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.3821.59615359
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.087 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 126 -
Rwork0.235 13984 -
obs--99.64 %
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)
11.99341.5727-0.28542.3426-0.09950.6119-0.17840.4099-0.1156-0.4880.1635-0.10440.0498-0.00840.01490.25190.00480.02290.2366-0.03990.067517.904461.03985.4411
26.1342-0.19070.35630.70790.22340.46040.0755-0.1699-0.57270.0976-0.03020.03070.2596-0.0746-0.04530.2233-0.00340.01510.14780.01760.06930.587349.451487.565
31.2412-0.2089-0.10561.77670.43510.8493-0.00910.026-0.340.0172-0.0065-0.11010.22880.07580.01550.07150.01930.01220.0144-0.0080.11310.775535.050835.1966
41.5224-0.4776-0.35481.58830.37980.7705-0.01840.0106-0.2097-0.02380.0172-0.22140.1360.16980.00120.04120.03410.01250.0451-0.00440.08730.378546.192635.3047
51.7971-0.3057-0.44661.21780.13430.7888-0.006-0.0285-0.0656-0.01860.0073-0.33180.03680.2213-0.00130.01470.01360.01160.06870.00110.105942.033265.520235.4061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A382 - 436
2X-RAY DIFFRACTION1B382 - 436
3X-RAY DIFFRACTION1C382 - 435
4X-RAY DIFFRACTION2A243 - 288
5X-RAY DIFFRACTION2B243 - 288
6X-RAY DIFFRACTION2C243 - 288
7X-RAY DIFFRACTION3A24 - 242
8X-RAY DIFFRACTION3A289 - 381
9X-RAY DIFFRACTION3A500
10X-RAY DIFFRACTION4B26 - 242
11X-RAY DIFFRACTION4B289 - 381
12X-RAY DIFFRACTION4B500
13X-RAY DIFFRACTION5C27 - 242
14X-RAY DIFFRACTION5C289 - 381
15X-RAY DIFFRACTION5C500

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