[English] 日本語
Yorodumi
- PDB-5v23: SeMet crystal structure of the Neisseria meningitidis non-core mi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v23
TitleSeMet crystal structure of the Neisseria meningitidis non-core minor pilin PilV in the orthorhombic form
ComponentsType IV pilin protein
KeywordsCELL ADHESION / pilin / minor pilin / type IV pili / Neisseria meningitidis
Function / homologyType IV pilus non-core minor pilin PilE-like / Type IV minor pilin ComP, DNA uptake sequence receptor / type IV pilus assembly / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / Type IV pilin protein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.956 Å
AuthorsKolappan, S. / Craig, L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP125959 Canada
CitationJournal: To Be Published
Title: SeMet structure of the non-core minor pilin PilV from Neisseria meningitidis in the orthorhombic form
Authors: Kolappan, S. / Craig, L.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type IV pilin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4004
Polymers11,1241
Non-polymers2763
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)21.794, 39.343, 109.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Type IV pilin protein


Mass: 11124.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: A6L27_01160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1ZB31
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 8000, ammonium chloride, sodium acetate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.976047, 0.979412
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9760471
20.9794121
ReflectionResolution: 1.956→54.81 Å / Num. obs: 7263 / % possible obs: 98.7 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.026 / Net I/σ(I): 23.9
Reflection shellResolution: 1.96→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 5.5 / Num. unique all: 442 / CC1/2: 0.981 / Rpim(I) all: 0.129 / % possible all: 89.2

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.956→37.03 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.24
RfactorNum. reflection% reflection
Rfree0.2545 371 5.14 %
Rwork0.1846 --
obs0.1884 7217 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.956→37.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 18 73 864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007824
X-RAY DIFFRACTIONf_angle_d0.9321111
X-RAY DIFFRACTIONf_dihedral_angle_d16.705502
X-RAY DIFFRACTIONf_chiral_restr0.048120
X-RAY DIFFRACTIONf_plane_restr0.005146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9556-2.23850.26561080.18052181X-RAY DIFFRACTION97
2.2385-2.82010.28881250.20282273X-RAY DIFFRACTION99
2.8201-37.03650.23741380.17752392X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.3261 Å / Origin y: 15.2013 Å / Origin z: 70.6041 Å
111213212223313233
T0.1712 Å20.0098 Å20.0354 Å2-0.1332 Å20.0162 Å2--0.1255 Å2
L0.6047 °20.535 °2-0.2072 °2-2.1784 °2-0.5477 °2--0.8871 °2
S-0.0482 Å °0.034 Å °-0.0789 Å °-0.4822 Å °-0.0018 Å °-0.1802 Å °-0.0291 Å °-0.0256 Å °0.0009 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 25 through 122 )

+
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