[English] 日本語
Yorodumi
- PDB-5edj: Crystal structure of the Neisseria meningitidis iron-regulated ou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5edj
TitleCrystal structure of the Neisseria meningitidis iron-regulated outer membrane lipoprotein FrpD
ComponentsFrpC operon protein
KeywordsUNKNOWN FUNCTION / Iron-regulated protein FrpD / FrpC-binding protein / novel fold / membrane protein
Function / homologyRTX iron-regulated FrpC / RTX iron-regulated protein FrpC / Prokaryotic membrane lipoprotein lipid attachment site profile. / RTX iron-regulated protein (frpC) / FrpC operon protein
Function and homology information
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSviridova, E. / Bumba, L. / Rezacova, P. / Sebo, P. / Kuta Smatanova, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant AgencyP207/11/0717 Czech Republic
Citation
Journal: Sci Rep / Year: 2017
Title: Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.
Authors: Sviridova, E. / Rezacova, P. / Bondar, A. / Veverka, V. / Novak, P. / Schenk, G. / Svergun, D.I. / Kuta Smatanova, I. / Bumba, L.
#1: Journal: Acta Crystallographica Section F / Year: 2010
Title: Crystallization and preliminary crystallographic characterization of the iron-regulated outer membrane lipoprotein FrpD from Neisseria meningitidis
Authors: Sviridova, E. / Bumba, L. / Rezacova, P. / Prochazkova, K. / Kavan, D. / Bezoushka, K. / Kuty, M. / Sebo, P. / Kuta Smatanova, I.
History
DepositionOct 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Jan 10, 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: FrpC operon protein


Theoretical massNumber of molelcules
Total (without water)27,0281
Polymers27,0281
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.390, 115.390, 38.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein FrpC operon protein / RTX iron-regulated protein (frpC) / Iron-regulated protein FrpD


Mass: 27027.986 Da / Num. of mol.: 1 / Fragment: UNP residues 43-271
Source method: isolated from a genetically manipulated source
Details: Fragment FrpD43-271, where: 1. the sequence position present in the structure is 44-267; 2. LE sequence at the C-terminus is a cloning artifact
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: LA50_03295 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08840, UniProt: Q9K129*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13418 / Num. obs: 13324 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / % possible all: 95.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALEPACKdata scaling
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EDF

5edf


Resolution: 2.3→30.65 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.477 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24931 668 5 %RANDOM
Rwork0.18287 ---
obs0.18619 12627 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 2.3→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 130 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9342579
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26725106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.814158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211497
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.83361118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.28101822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6056781
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.35812757
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 39 -
Rwork0.241 855 -
obs--94.2 %
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)
12.11160.70050.43853.49030.84162.61870.0241-0.06370.14570.1312-0.023-0.1687-0.06930.0707-0.00110.190.02840.00850.15720.03570.1491-25.62642.0271.616
21.54260.2248-1.26194.0091.04033.3353-0.0315-0.046-0.05990.343-0.09770.19660.0865-0.19190.12920.2375-0.00140.00490.17240.0380.1196-29.70829.953.121
33.24550.8327-1.87497.11691.01236.0037-0.1834-0.165-0.2355-0.58890.3065-0.28690.20140.4422-0.12310.223-0.0902-0.00660.1874-0.02670.1329-31.5276.201-13.464
42.9645-0.3560.91844.2939-0.90346.95850.18350.0513-0.1076-0.0721-0.16930.21430.58560.2266-0.01420.2302-0.05980.02710.13320.02070.1557-30.8875.513-5.594
50.5747-1.77741.654810.3074-10.413110.796-0.1534-0.0126-0.00270.2636-0.2966-0.3869-0.09370.11560.450.399-0.10990.0210.26030.03650.2258-28.2918.1243.862
61.41331.73880.83986.26210.18391.0971-0.00750.12870.06050.20580.0230.3951-0.0264-0.178-0.01560.2237-0.02760.0510.21050.00790.1279-32.74622.734-3.684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 94
2X-RAY DIFFRACTION2A95 - 153
3X-RAY DIFFRACTION3A154 - 173
4X-RAY DIFFRACTION4A174 - 200
5X-RAY DIFFRACTION5A201 - 220
6X-RAY DIFFRACTION6A221 - 267

+
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