[English] 日本語
Yorodumi
- PDB-6cuj: Crystal structure of the C-terminal domain of neisserial heparin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cuj
TitleCrystal structure of the C-terminal domain of neisserial heparin binding antigen (NHBA)
ComponentsGna2132
KeywordsLIPID BINDING PROTEIN / Vaccine / Neisseria / Meningitis / Disorder
Function / homologyTransferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / heparin binding / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell adhesion / DNA binding / Neisserial heparin binding antigen
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 Å
AuthorsMalito, E. / Spraggon, G.
CitationJournal: PLoS ONE / Year: 2018
Title: Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody.
Authors: Maritan, M. / Veggi, D. / Cozzi, R. / Dello Iacono, L. / Bartolini, E. / Lo Surdo, P. / Maruggi, G. / Spraggon, G. / Bottomley, M.J. / Malito, E.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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: Gna2132
B: Gna2132


Theoretical massNumber of molelcules
Total (without water)34,7542
Polymers34,7542
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-3 kcal/mol
Surface area13750 Å2
Unit cell
Length a, b, c (Å)77.030, 77.030, 57.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Gna2132 / Heparin binding protein / Neisserial heparin binding antigen / Putative lipoprotein GNA2132 / ...Heparin binding protein / Neisserial heparin binding antigen / Putative lipoprotein GNA2132 / Transferrin-binding protein-like solute binding protein


Mass: 17377.043 Da / Num. of mol.: 2 / Fragment: UNP Residues 133-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna2132, nhba, A6J54_02980 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9JPP1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe full sequence MAANGGSNFGRVDLANGVLIDGPSQNITLTHSKGDSSNGDNLLDEEAPSKSEFENLNESERIEKYKKDGKSDKFTNLVAT ...The full sequence MAANGGSNFGRVDLANGVLIDGPSQNITLTHSKGDSSNGDNLLDEEAPSKSEFENLNESERIEKYKKDGKSDKFTNLVAT AVQANGTNKYVIIYKDKSASSSSARFRRSARSRRSLPAEMPLIPVNQADTLIVDGEAVSLTGHSGNIFAPEGNYRYLTYG AEKLPGGSYALRVQGEPAKGEMLAGTAVYNGEVLHFHTENGRPYPTRGRFAAKVDFGSKSVDGIIDSGDDLHMGTQKFKA AIDGNGFKGTWTENGGGDVSGRFYGPAGEEVAGKYSYRPTDAEKGGFGVFAGKKEQDLEHHHHHH was crystallized. However, only residues 275-426 were visible in the crystal.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3,350, 0.2 M Sodium thiocyanate

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.8→46 Å / Num. obs: 31127 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 32.8 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.06 / Rsym value: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 5025 / CC1/2: 0.84 / Rsym value: 0.47 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LFU

2lfu


Resolution: 1.805→46 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2383 1555 5 %
Rwork0.1912 --
obs0.1935 31105 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.805→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 0 121 2367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072303
X-RAY DIFFRACTIONf_angle_d0.8973095
X-RAY DIFFRACTIONf_dihedral_angle_d3.2561309
X-RAY DIFFRACTIONf_chiral_restr0.062292
X-RAY DIFFRACTIONf_plane_restr0.006421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.805-1.86280.29441410.26242664X-RAY DIFFRACTION100
1.8628-1.92940.30481410.23092696X-RAY DIFFRACTION100
1.9294-2.00660.22791400.1982657X-RAY DIFFRACTION100
2.0066-2.0980.2241410.1892669X-RAY DIFFRACTION100
2.098-2.20860.25451410.18332686X-RAY DIFFRACTION100
2.2086-2.34690.25561410.18872665X-RAY DIFFRACTION100
2.3469-2.52810.22831410.1992694X-RAY DIFFRACTION100
2.5281-2.78250.24871410.19992667X-RAY DIFFRACTION100
2.7825-3.18510.23751410.19312701X-RAY DIFFRACTION100
3.1851-4.01250.231430.1792708X-RAY DIFFRACTION100
4.0125-50.22731440.18552743X-RAY DIFFRACTION99

+
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