[English] 日本語
Yorodumi
- PDB-4aip: The FrpB iron transporter from Neisseria meningitidis (F3-3 variant) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aip
TitleThe FrpB iron transporter from Neisseria meningitidis (F3-3 variant)
ComponentsFE-REGULATED PROTEIN B
KeywordsTRANSPORT PROTEIN / OUTER MEMBRANE / TONB-DEPENDENT TRANSPORTER
Function / homology
Function and homology information


: / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel ...TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Fe-regulated protein B
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSaleem, M. / Prince, S.M. / Derrick, J.P.
Citation
Journal: Plos One / Year: 2013
Title: Use of a Molecular Decoy to Segregate Transport from Antigenicity in the Frpb Iron Transporter from Neisseria Meningitidis
Authors: Saleem, M. / Prince, S.M. / Rigbb, S.E.J. / Imran, M. / Patel, H. / Chan, H. / Sanders, H. / Maiden, M.C.J. / Feavers, I.M. / Derrick, J.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Refolding, Purification and Crystallization of the Frpb Outer Membrane Iron Transporter from Neisseria Meningitidis.
Authors: Saleem, M. / Prince, S.M. / Patel, H. / Chan, H. / Feavers, I.M. / Derrick, J.P.
History
DepositionFeb 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references / Structure summary
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FE-REGULATED PROTEIN B
B: FE-REGULATED PROTEIN B
C: FE-REGULATED PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,8216
Polymers246,9733
Non-polymers8483
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-46.8 kcal/mol
Surface area76590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.320, 104.620, 269.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLYSLYSAA62 - 31862 - 318
21ARGARGLYSLYSBB62 - 31862 - 318
31ARGARGLYSLYSCC62 - 31862 - 318
12LYSLYSLEULEUAA325 - 395325 - 395
22LYSLYSLEULEUBB325 - 395325 - 395
32LYSLYSLEULEUCC325 - 395325 - 395
13LYSLYSASNASNAA433 - 565433 - 565
23LYSLYSASNASNBB433 - 565433 - 565
33LYSLYSASNASNCC433 - 565433 - 565
14GLUGLUPHEPHEAA577 - 742577 - 742
24GLUGLUPHEPHEBB577 - 742577 - 742
34GLUGLUPHEPHECC577 - 742577 - 742

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.8235, -0.3203, 0.4682), (0.2677, -0.5083, -0.8185), (0.5002, 0.7994, -0.3329)22.39, 18.25, -60.46
2given(0.8377, 0.295, 0.4597), (-0.2733, -0.5023, 0.8204), (0.4729, -0.8128, -0.3402)6.709, 65.6, -14.64

-
Components

#1: Protein FE-REGULATED PROTEIN B


Mass: 82324.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Plasmid: PET30EKLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): T7 EXPRESS / References: UniProt: Q51162
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-N8E / 3,6,9,12,15-PENTAOXATRICOSAN-1-OL / N-OCTYLPENTAOXYETHYLENE / PENTAETHYLENE GLYCOL MONOOCTYL ETHER / OCTYLPENTAGLYCOL N-OCTYLPENTAOXYETHYLENE


Mass: 350.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3,6,9,12,15-PENTAOXATRICOSAN-1-OL (N8E): DETERGENT MOLECULE
Sequence detailsDEVIATION AT N-TERMINUS DUE TO ADDITION OF PURIFICATION TAG AND REMOVAL OF SIGNAL SEQUENCE FROM THE ...DEVIATION AT N-TERMINUS DUE TO ADDITION OF PURIFICATION TAG AND REMOVAL OF SIGNAL SEQUENCE FROM THE EXPRESSION CONSTRUCT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6
Details: 0.6% (W/V) HEXYL-B-D-MALTOSIDE, 20 MM NA L-GLUTAMATE, 20 MM D, L-ALANINE, 20 MM GLYCINE, 20 MM LYSINE (RACEMIC), 20 MM SERINE (RACEMIC), 29 MM IMIDAZOLE, 11.6% (V/V) MPD, 11.6% (W/V) PEG ...Details: 0.6% (W/V) HEXYL-B-D-MALTOSIDE, 20 MM NA L-GLUTAMATE, 20 MM D, L-ALANINE, 20 MM GLYCINE, 20 MM LYSINE (RACEMIC), 20 MM SERINE (RACEMIC), 29 MM IMIDAZOLE, 11.6% (V/V) MPD, 11.6% (W/V) PEG 1000, 11.6% (W/V) PEG 3350 AND 71 MM MES (PH 6.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→134 Å / Num. obs: 86235 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.2
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 83.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FHH

3fhh


Resolution: 2.4→134.55 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.836 / SU B: 10.807 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.58 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-59, 401-416, 568-573 AND 673-675 OMITTED FROM SOME OR ALL CHAINS DUE TO POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29639 4301 5 %RANDOM
Rwork0.24183 ---
obs0.24456 81658 90.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.534 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→134.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15599 0 58 328 15985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02115978
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1361.93221551
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67151981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13823.845814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.304152638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.84815123
X-RAY DIFFRACTIONr_chiral_restr0.1430.22262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112407
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_it1.5291.59804
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.852215652
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.76536174
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7074.55899
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1028tight positional0.070.05
12B1028tight positional0.050.05
13C1028tight positional0.070.05
21A284tight positional0.070.05
22B284tight positional0.060.05
23C284tight positional0.070.05
31A532tight positional0.060.05
32B532tight positional0.050.05
33C532tight positional0.070.05
41A648tight positional0.150.05
42B648tight positional0.170.05
43C648tight positional0.190.05
11A942loose positional0.235
12B942loose positional0.165
13C942loose positional0.245
21A284loose positional0.245
22B284loose positional0.165
23C284loose positional0.245
31A516loose positional0.075
32B516loose positional0.075
33C516loose positional0.085
41A639loose positional0.475
42B639loose positional0.375
43C639loose positional0.365
11A1028tight thermal0.170.5
12B1028tight thermal0.180.5
13C1028tight thermal0.180.5
21A284tight thermal0.160.5
22B284tight thermal0.160.5
23C284tight thermal0.150.5
31A532tight thermal0.170.5
32B532tight thermal0.170.5
33C532tight thermal0.150.5
41A648tight thermal2.380.5
42B648tight thermal4.040.5
43C648tight thermal3.010.5
11A942loose thermal0.1710
12B942loose thermal0.1710
13C942loose thermal0.1710
21A284loose thermal0.1810
22B284loose thermal0.1610
23C284loose thermal0.1710
31A516loose thermal0.1610
32B516loose thermal0.1610
33C516loose thermal0.1610
41A639loose thermal3.610
42B639loose thermal4.6510
43C639loose thermal4.0910
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 286 -
Rwork0.338 5470 -
obs--82.9 %

+
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