[English] 日本語
Yorodumi
- PDB-5nqy: Structure of a fHbp(V1.4):PorA(P1.16) chimera. Fusion at fHbp pos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nqy
TitleStructure of a fHbp(V1.4):PorA(P1.16) chimera. Fusion at fHbp position 309.
ComponentsFactor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001
KeywordsIMMUNE SYSTEM / Meningitis / Vaccine / Complement / Chimeric
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Immunoglobulin-like - #1980 / Porin, Neisseria sp. type / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Porin - #90 / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. ...Immunoglobulin-like - #1980 / Porin, Neisseria sp. type / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Porin - #90 / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / : / Porin domain superfamily / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major outer membrane protein P.IA / Factor H binding protein variant B16_001
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Neisseria meningitidis serogroup C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJohnson, S. / Hollingshead, S. / Lea, S.M. / Tang, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0900888 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structure-based design of chimeric antigens for multivalent protein vaccines.
Authors: Hollingshead, S. / Jongerius, I. / Exley, R.M. / Johnson, S. / Lea, S.M. / Tang, C.M.
History
DepositionApr 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001


Theoretical massNumber of molelcules
Total (without water)29,3201
Polymers29,3201
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.850, 62.640, 88.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001 / Factor H binding protein variant B16_002 / Factor H binding protein variant B16_003 / Factor H ...Factor H binding protein variant B16_002 / Factor H binding protein variant B16_003 / Factor H binding protein variant B16_004 / Factor H binding protein variant B16_005 / Factor H binding protein variant B16_006 / Putative lipoprotein / Protein IA / Class 1 protein / Factor H binding protein variant B16_002 / Factor H binding protein variant B16_003 / Factor H binding protein variant B16_004 / Factor H binding protein variant B16_005 / Factor H binding protein variant B16_006 / Putative lipoprotein


Mass: 29319.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria), (gene. exp.) Neisseria meningitidis serogroup C (bacteria)
Gene: fhbp, porA / Variant: V1.4 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: Q6VS06, UniProt: P13415
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2M potassium formate, 20%(w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.6→51.17 Å / Num. obs: 10208 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.032 / Net I/σ(I): 16.7
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 743 / Rpim(I) all: 0.356 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ayd

4ayd


Resolution: 2.6→51.165 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.78
RfactorNum. reflection% reflection
Rfree0.2708 498 4.9 %
Rwork0.2264 --
obs0.2285 10163 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→51.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 0 4 2002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022030
X-RAY DIFFRACTIONf_angle_d0.4492730
X-RAY DIFFRACTIONf_dihedral_angle_d9.4081218
X-RAY DIFFRACTIONf_chiral_restr0.042300
X-RAY DIFFRACTIONf_plane_restr0.003360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.86180.421200.3512369X-RAY DIFFRACTION99
2.8618-3.27590.33931150.30252377X-RAY DIFFRACTION99
3.2759-4.1270.27791280.23142387X-RAY DIFFRACTION100
4.127-51.17520.21881350.17952532X-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)
13.9940.25370.161.67290.582.0880.15480.1711-0.0978-0.1313-0.0673-0.31980.18150.3547-0.10430.71260.0550.0790.5450.06130.62434.4842-3.079450.6213
22.8976-0.04711.20471.61231.36176.39840.0398-0.28880.0397-0.2019-0.08470.0794-0.1694-0.59490.01070.59180.03170.09490.47470.02960.49713.81981.872254.9717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 79 through 201 )
2X-RAY DIFFRACTION2chain 'A' and (resid 202 through 328 )

+
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://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