[English] 日本語
Yorodumi
- PDB-7nru: Structure of a natural chimera of meningococcal factor H binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nru
TitleStructure of a natural chimera of meningococcal factor H binding protein belonging to NL096 strain
ComponentsFactor H binding protein variant 1-2,3.x
KeywordsPROTEIN BINDING / meningococcal antigen / natural chimera
Function / homologyFactor H binding protein, C-terminal / Factor H binding protein, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Factor H binding protein variant A62_001
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21998357323 Å
AuthorsVeggi, D. / Malito, E. / Bottomley, M.J.
Citation
Journal: Comput Struct Biotechnol J / Year: 2022
Title: Structural characterization of a cross-protective natural chimera of factor H binding protein from meningococcal serogroup B strain NL096.
Authors: Veggi, D. / Malito, E. / Lo Surdo, P. / Pansegrau, W. / Rippa, V. / Wahome, N. / Savino, S. / Masignani, V. / Pizza, M. / Bottomley, M.J.
#1: Journal: Patent / Year: 2020
Title: Neisseria meningitidis compositions and methods thereof
Authors: Jansen, K.U. / Anderson, A.S. / Absalon, J. / Aste-Amezaga, J.M. / Beeslaar, J.F. / Cooper, D. / Farley, J.E. / Fletcher, L.D. / Harris, S.L. / Jones, T.R. / Kanevsky, I. / Khandke, L. / ...Authors: Jansen, K.U. / Anderson, A.S. / Absalon, J. / Aste-Amezaga, J.M. / Beeslaar, J.F. / Cooper, D. / Farley, J.E. / Fletcher, L.D. / Harris, S.L. / Jones, T.R. / Kanevsky, I. / Khandke, L. / Liberator, P. / Perez, J.L. / Phelan, L.M. / Zlotnick, G.W.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Factor H binding protein variant 1-2,3.x
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0923
Polymers27,9001
Non-polymers1922
Water4,756264
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-14 kcal/mol
Surface area11900 Å2
Unit cell
Length a, b, c (Å)125.680, 42.610, 44.410
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Factor H binding protein variant 1-2,3.x / Factor H binding protein variant A62_001 / Factor H binding protein variant A62_002


Mass: 27900.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: fhbp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0JF81
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M tri-sodium citrate, 3.2M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.219→23.37 Å / Num. obs: 65693 / % possible obs: 95.2 % / Redundancy: 3 % / Biso Wilson estimate: 10.1827524357 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.5
Reflection shellResolution: 1.22→1.264 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 9280

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KVD

3kvd


Resolution: 1.21998357323→23.3683816098 Å / SU ML: 0.0836274587195 / Cross valid method: FREE R-VALUE / σ(F): 1.3571381526 / Phase error: 15.1064659749
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.165911504385 3315 5.04996648589 %
Rwork0.141822105155 62329 -
obs0.143044838589 65644 95.1983177435 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.576031317 Å2
Refinement stepCycle: LAST / Resolution: 1.21998357323→23.3683816098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 10 264 2091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01120101094831939
X-RAY DIFFRACTIONf_angle_d1.156915051162621
X-RAY DIFFRACTIONf_chiral_restr0.0971800465012292
X-RAY DIFFRACTIONf_plane_restr0.00710912870033345
X-RAY DIFFRACTIONf_dihedral_angle_d12.6975346417739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.23740.192595162611200.1640855721332495X-RAY DIFFRACTION91.9479606188
1.2374-1.25590.1621593432441460.1560242467382515X-RAY DIFFRACTION92.0124481328
1.2559-1.27550.2003210430491340.1509754653892474X-RAY DIFFRACTION92.1554770318
1.2755-1.29640.1690537204141330.1458353291872535X-RAY DIFFRACTION92.9940745904
1.2964-1.31880.210263198421450.1445053985792506X-RAY DIFFRACTION93.5426958363
1.3188-1.34270.1894748744471460.1408924539182568X-RAY DIFFRACTION94.1380506417
1.3427-1.36860.1586481316671090.1391746178452534X-RAY DIFFRACTION93.3262711864
1.3686-1.39650.1720653247361210.1346231877462508X-RAY DIFFRACTION91.475295755
1.3965-1.42690.1636547248481580.131837145012548X-RAY DIFFRACTION95.0140449438
1.4269-1.460.1733598586151450.1254866338242578X-RAY DIFFRACTION95.2764170749
1.46-1.49660.1677858357391430.1302329813122603X-RAY DIFFRACTION96.1148057403
1.4966-1.5370.1521235426191510.1221697368782613X-RAY DIFFRACTION95.7063711911
1.537-1.58220.1417058654841290.1224230089432626X-RAY DIFFRACTION96.0264900662
1.5822-1.63330.1460672484741280.1227467557122623X-RAY DIFFRACTION96.2898144907
1.6333-1.69160.1611014019391340.1290169786082562X-RAY DIFFRACTION94.7960618847
1.6916-1.75940.1708827618721720.1315075244042609X-RAY DIFFRACTION96.4285714286
1.7594-1.83940.1692732817291130.1350346987372586X-RAY DIFFRACTION94.2388268156
1.8394-1.93630.1720330636621230.1343560479192623X-RAY DIFFRACTION94.6896551724
1.9363-2.05760.1373396467511420.1236789632642660X-RAY DIFFRACTION98.4193888303
2.0576-2.21630.1551965826651630.126560305292675X-RAY DIFFRACTION98.2686980609
2.2163-2.43920.1604702658821200.1412172186152703X-RAY DIFFRACTION98.0548801667
2.4392-2.79160.1632828936451440.1530238394672685X-RAY DIFFRACTION97.2164948454
2.7916-3.51520.1728381384841580.1582185873062674X-RAY DIFFRACTION96.9863013699
3.5152-23.3680.1744252987291380.1579604363992826X-RAY DIFFRACTION99.4964753273

+
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