[English] 日本語
Yorodumi
- PDB-5ngd: Crystal structure of the V325G mutant of the bacteriophage G20C p... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more