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- PDB-4e27: Crystal Structure of a Pentameric Capsid Protein Isolated from Me... -

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Basic information

Entry
Database: PDB / ID: 4.0E+27
TitleCrystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences Solved by Iodide SAD Phasing
ComponentsCapsid ProteinCapsid
KeywordsVIRAL PROTEIN / Capsid Protein
Function / homologyJelly Rolls - #1010 / Jelly Rolls / Sandwich / Mainly Beta / IODIDE ION
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.4 Å
AuthorsCraig, T.K. / Abendroth, J. / Lorimer, D. / Burgin Jr, A.B. / Segall, A. / Rohwer, F.
CitationJournal: To be Published
Title: Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences Solved by Iodide SAD Phasing
Authors: Craig, T.K. / Abendroth, J. / Lorimer, D. / Burgin Jr, A.B. / Segall, A. / Rohwer, F.
History
DepositionMar 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Derived calculations
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_asym_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_asym_id / _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_asym_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_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: Capsid Protein
B: Capsid Protein
C: Capsid Protein
D: Capsid Protein
E: Capsid Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,35534
Polymers92,7785
Non-polymers3,57629
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25750 Å2
ΔGint-122 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.710, 68.360, 107.830
Angle α, β, γ (deg.)90.00, 93.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-314-

HOH

21C-384-

HOH

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Components

#1: Protein
Capsid Protein / Capsid


Mass: 18555.656 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pEMB009 VCID5936 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 293 K / pH: 7
Details: 20% PEG 3350, 0.2M K Formate, no buffer, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 14, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 75296 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.25 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.39
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.88 / % possible all: 99.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MLPHAREphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.51 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.33 / σ(F): 2 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1947 5.03 %
Rwork0.202 --
obs0.205 38729 99.8 %
all-38729 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.05 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.6516 Å2-0 Å2-0.8773 Å2
2---2.7902 Å20 Å2
3---4.4418 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5654 0 29 488 6171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075837
X-RAY DIFFRACTIONf_angle_d1.0817966
X-RAY DIFFRACTIONf_dihedral_angle_d12.4262072
X-RAY DIFFRACTIONf_chiral_restr0.0711028
X-RAY DIFFRACTIONf_plane_restr0.0041048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.46020.32511680.25042630X-RAY DIFFRACTION100
2.4602-2.52670.26431280.21022601X-RAY DIFFRACTION100
2.5267-2.60110.29681220.22432623X-RAY DIFFRACTION100
2.6011-2.6850.29571380.21072577X-RAY DIFFRACTION100
2.685-2.7810.28251240.21242656X-RAY DIFFRACTION100
2.781-2.89230.27151260.18812609X-RAY DIFFRACTION100
2.8923-3.02390.291420.21922598X-RAY DIFFRACTION98
3.0239-3.18330.27661360.19962595X-RAY DIFFRACTION99
3.1833-3.38260.22931370.19162624X-RAY DIFFRACTION100
3.3826-3.64370.21651580.192626X-RAY DIFFRACTION100
3.6437-4.01010.24821380.18492651X-RAY DIFFRACTION100
4.0101-4.58990.16661200.15122646X-RAY DIFFRACTION100
4.5899-5.78060.23111610.18782634X-RAY DIFFRACTION100
5.7806-43.51690.33081490.27862712X-RAY DIFFRACTION100
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)
10.5689-0.0404-0.26620.525-0.49470.62950.16340.020.00550.18160.0234-0.04770.18280.08330.07210.37420.0233-0.11820.40720.07810.236149.052-16.98853.725
20.0334-0.05610.0110.56250.07150.47970.0175-0.2202-0.2030.2659-0.0059-0.17940.18550.21650.34070.20020.0437-0.05120.17580.07420.147444.8353-21.14828.89
30.2908-0.08190.02870.1835-0.05830.09670.0163-0.0331-0.1020.0208-0.0270.03950.04440.0113-0.02090.0724-0.00080.00550.01560.03350.078420.5267-31.233119.6419
40.17020.0506-0.27890.0223-0.10550.5278-0.0234-0.31080.33280.22440.11290.107-0.35-0.0435-0.06210.5782-0.1488-0.14620.48270.0820.481653.47722.607141.9979
50.5197-0.00910.41620.1252-0.0640.3587-0.0456-0.12190.02760.0125-0.0633-0.07030.070.1745-0.17370.2256-0.0169-0.00040.34340.03390.096443.2513-15.355944.1026
60.1508-0.0312-0.07270.23440.02440.321-0.009-0.04590.0480.0915-0.01250.0268-0.0334-0.05890.01050.06510.00430.01010.0305-0.03140.054613.411-0.119527.2505
71.11060.2316-0.72240.0517-0.15860.48850.0108-0.23320.05760.2662-0.08270.18220.0848-0.08280.00410.4830.0326-0.04930.52750.01420.333354.402-29.64946.437
84.80560.48030.28950.45130.53821.70830.0076-0.2461-0.21970.2299-0.05390.18370.1547-0.13920.07070.48250.1376-0.16680.484-0.05150.318257.615-26.06946.389
90.7557-0.07591.26410.0925-0.19312.167-0.09680.03730.21750.2032-0.1084-0.2559-0.03170.41390.03460.13970.032-0.050.20070.01320.175147.6072-8.768436.1759
100.22380.0028-0.01050.20260.0420.1243-0.00570.03420.0016-0.00130.0029-0.0080.00390.0054-0.0121-0.00170.0290.01940.05180.00260.038631.8248-19.16677.9461
110.42380.16010.32860.29070.02420.2979-0.1354-0.08570.14390.1854-0.0488-0.14920.10340.2077-0.05720.16910.0353-0.02260.28240.02950.099948.4948-10.932538.8826
120.16510.0487-0.0350.26310.07380.2269-0.0070.00130.03740.0202-0.01170.019-0.02860.0087-0.00750.014-0.0368-0.01650.03080.01220.050527.44170.060512.6416
130.7018-0.1284-0.09420.32430.21720.502-0.1156-0.27940.4280.2451-0.03530.0365-0.22460.06370.01850.45990.0539-0.04190.6252-0.01250.338451.8254-5.633350.2504
140.37330.13750.2951.1410.09480.24910.0821-0.4742-0.08050.35010.0204-0.1750.03240.19380.08120.24740.0092-0.04930.25120.01130.081836.2576-25.293538.7068
150.2345-0.04560.04090.2658-0.10170.23740.0067-0.0728-0.01070.07220.01180.08290.0303-0.0411-0.0090.0548-0.00580.04450.07240.03560.04349.1404-19.454431.5994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:44)
2X-RAY DIFFRACTION2chain 'A' and (resseq 45:58)
3X-RAY DIFFRACTION3chain 'A' and (resseq 59:176)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:31)
5X-RAY DIFFRACTION5chain 'B' and (resseq 32:58)
6X-RAY DIFFRACTION6chain 'B' and (resseq 59:176)
7X-RAY DIFFRACTION7chain 'C' and (resseq 4:19)
8X-RAY DIFFRACTION8chain 'C' and (resseq 20:35)
9X-RAY DIFFRACTION9chain 'C' and (resseq 36:58)
10X-RAY DIFFRACTION10chain 'C' and (resseq 59:176)
11X-RAY DIFFRACTION11chain 'D' and (resseq 4:58)
12X-RAY DIFFRACTION12chain 'D' and (resseq 59:176)
13X-RAY DIFFRACTION13chain 'E' and (resseq 2:45)
14X-RAY DIFFRACTION14chain 'E' and (resseq 46:58)
15X-RAY DIFFRACTION15chain 'E' and (resseq 59:176)

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