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- PDB-5ngd: Crystal structure of the V325G mutant of the bacteriophage G20C p... -

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Basic information

Entry
Database: PDB / ID: 5ngd
TitleCrystal structure of the V325G mutant of the bacteriophage G20C portal protein
ComponentsPortal protein
KeywordsTRANSPORT PROTEIN / G20C / portal protein / bacteriophage
Function / homologyPortal protein
Function and homology information
Biological speciesThermus phage P7426 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPascoa, T. / Jenkins, H.T. / Chechik, M. / Greive, S.J. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Bilateral NSF/BIO-BBSRCBB/N018729/1 United Kingdom
Wellcome Trust101528/Z/13/Z United Kingdom
CitationJournal: Acs Nano / Year: 2017
Title: Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization
Authors: Cressiot, B. / Greive, S.J. / Si, W. / Pascoa, T.C. / Mojtabavi, M. / Chechik, M. / Jenkins, H.T. / Lu, X. / Aksimentiev, A. / Antson, A.A. / Wanunu, M.
History
DepositionMar 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
D: Portal protein


Theoretical massNumber of molelcules
Total (without water)183,9274
Polymers183,9274
Non-polymers00
Water12,665703
1
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein

A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein

A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein


Theoretical massNumber of molelcules
Total (without water)551,78112
Polymers551,78112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area123900 Å2
ΔGint-762 kcal/mol
Surface area159420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.234, 223.234, 115.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA29 - 4348 - 413
21ARGARGBB29 - 4348 - 413
12ARGARGAA29 - 4348 - 413
22ARGARGCC29 - 4348 - 413
13GLNGLNAA29 - 4358 - 414
23GLNGLNDD29 - 4358 - 414
14GLNGLNBB29 - 4358 - 414
24GLNGLNCC29 - 4358 - 414
15ARGARGBB29 - 4348 - 413
25ARGARGDD29 - 4348 - 413
16ARGARGCC29 - 4348 - 413
26ARGARGDD29 - 4348 - 413

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Portal protein


Mass: 45981.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage P7426 (virus) / Gene: P74p85 / Production host: Escherichia coli (E. coli) / References: UniProt: A7XXR3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 3.04 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein in 1 M NaCl, 20 mM Tris pH 7.5. Reservoir: 0.1 M Imidazole HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97883 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 1.9→111.62 Å / Num. obs: 165587 / % possible obs: 97.8 % / Redundancy: 2.1 % / CC1/2: 0.943 / Rmerge(I) obs: 0.168 / Net I/σ(I): 3.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8194 / CC1/2: 0.401 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→111.62 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.308 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22512 1623 1 %RANDOM
Rwork0.20605 ---
obs0.20623 164209 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å2-0 Å2
2--0.3 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 1.9→111.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12337 0 0 703 13040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01912643
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211917
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.96617226
X-RAY DIFFRACTIONr_angle_other_deg1.019327537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40351613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42124.335526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.299152038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6821561
X-RAY DIFFRACTIONr_chiral_restr0.1040.21984
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022524
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_it1.0441.6686434
X-RAY DIFFRACTIONr_mcbond_other1.0441.6676433
X-RAY DIFFRACTIONr_mcangle_it1.6942.4938032
X-RAY DIFFRACTIONr_mcangle_other1.6942.4938033
X-RAY DIFFRACTIONr_scbond_it1.4011.8376209
X-RAY DIFFRACTIONr_scbond_other1.4011.8376210
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2452.6949188
X-RAY DIFFRACTIONr_long_range_B_refined3.76520.2614115
X-RAY DIFFRACTIONr_long_range_B_other3.72220.0813989
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A24218
12B24218
21A24242
22C24242
31A24384
32D24384
41B24280
42C24280
51B24222
52D24222
61C24378
62D24378
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 117 -
Rwork0.298 12111 -
obs--97.24 %
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)
11.1263-0.84740.15341.2944-0.36980.27960.10120.3072-0.0273-0.2421-0.1134-0.02310.04020.04340.01220.16560.0050.00860.179-0.02040.0732-94.5247208.1417-50.7404
21.00840.1466-0.0412.6123-0.09260.54570.0252-0.127-0.03960.1581-0.0498-0.4587-0.00120.10.02460.15050.0105-0.02750.20660.01410.0809-86.7896190.641229.5817
30.9865-0.0303-0.04530.7786-0.04210.60410.00180.0821-0.0091-0.00950.0092-0.17310.01030.181-0.0110.01430.0086-0.00490.0666-0.01250.0426-68.5074186.1898-20.7128
40.92780.0435-0.08250.8144-0.14880.6588-0.00620.06740.05160.00880.0083-0.1515-0.06670.1746-0.00210.0263-0.0133-0.01020.0601-0.00810.0391-70.8453208.7183-20.6322
50.7996-0.02920.0990.7455-0.14940.6062-0.00590.00970.16950.01180.0068-0.0719-0.12510.1071-0.0010.0375-0.02550.00130.0224-0.00450.0453-83.8199227.2429-20.5958
60.59650.0851-0.07860.8616-0.3860.70940.0093-0.04410.16110.046-0.00620.0061-0.1440.0039-0.0030.041-0.0006-0.0020.0033-0.01190.0442-104.4622236.6421-20.7704
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A382 - 435
2X-RAY DIFFRACTION1B382 - 435
3X-RAY DIFFRACTION1C382 - 435
4X-RAY DIFFRACTION1D382 - 436
5X-RAY DIFFRACTION2A243 - 288
6X-RAY DIFFRACTION2B243 - 288
7X-RAY DIFFRACTION2C243 - 288
8X-RAY DIFFRACTION2D243 - 288
9X-RAY DIFFRACTION3A29 - 242
10X-RAY DIFFRACTION3A289 - 381
11X-RAY DIFFRACTION4B29 - 242
12X-RAY DIFFRACTION4B289 - 381
13X-RAY DIFFRACTION5C29 - 242
14X-RAY DIFFRACTION5C289 - 381
15X-RAY DIFFRACTION6D28 - 242
16X-RAY DIFFRACTION6D289 - 381

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