[English] 日本語
Yorodumi
- PDB-4b8y: Ferrichrome-bound FhuD2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b8y
TitleFerrichrome-bound FhuD2
Components
  • FHUD2
  • VIRULENCE FACTOR
KeywordsTRANSPORT PROTEIN/SIDEROPHORE / TRANSPORT PROTEIN-SIDEROPHORE COMPLEX / TRANSPORT PROTEIN / VACCINE / SIDEROPHORE / CLASS III SOLUTE BINDING / INHIBITOR PROTEIN (SBP)
Function / homology
Function and homology information


outer membrane-bounded periplasmic space
Similarity search - Function
ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Fe/B12 periplasmic-binding domain-containing protein
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMalito, E. / Bottomley, M.J. / Spraggon, G.
CitationJournal: Biochem.J. / Year: 2013
Title: Structural and Functional Characterization of the Staphylococcus Aureus Virulence Factor and Vaccine Candidate Fhud2.
Authors: Mariotti, P. / Malito, E. / Biancucci, M. / Lo Surdo, P. / Mishra, R.P. / Nardi-Dei, V. / Savino, S. / Nissum, M. / Spraggon, G. / Grandi, G. / Bagnoli, F. / Bottomley, M.J.
History
DepositionAug 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FHUD2
B: VIRULENCE FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,79414
Polymers32,0822
Non-polymers71212
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4.9 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.890, 50.140, 54.350
Angle α, β, γ (deg.)90.00, 106.44, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein FHUD2


Mass: 31375.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCTC 8325 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2FVW9
#2: Protein/peptide VIRULENCE FACTOR


Mass: 705.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

-
Non-polymers , 4 types, 138 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsCLONED WITHOUT THE SIGNAL PEPTIDE AND LIPOBOX MOTIF

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growpH: 8.5 / Details: 20% PEG-2000, 0.01M NICL2, 0.1M TRIS-HCL PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 22105 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 24.87 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G9Q

3g9q


Resolution: 1.9→36.137 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1094 4.9 %
Rwork0.1736 --
obs0.176 22086 99.88 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.905 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.9365 Å20 Å25.4556 Å2
2---2.4363 Å20 Å2
3----1.5002 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 42 126 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172333
X-RAY DIFFRACTIONf_angle_d1.3173086
X-RAY DIFFRACTIONf_dihedral_angle_d14.164888
X-RAY DIFFRACTIONf_chiral_restr0.083327
X-RAY DIFFRACTIONf_plane_restr0.006382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.98660.29861440.24312589X-RAY DIFFRACTION100
1.9866-2.09130.27591480.20052604X-RAY DIFFRACTION100
2.0913-2.22230.22841160.17282611X-RAY DIFFRACTION100
2.2223-2.39380.21561380.15332621X-RAY DIFFRACTION100
2.3938-2.63470.22781380.15892601X-RAY DIFFRACTION100
2.6347-3.01580.1991400.16712619X-RAY DIFFRACTION100
3.0158-3.79890.22081340.16132647X-RAY DIFFRACTION100
3.7989-36.14320.21291360.17992700X-RAY DIFFRACTION100
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)
10.2567-0.0090.15180.00160.00770.2317-0.0256-0.01960.07810.0170.07230.0037-0.0312-0.08350.23390.08650.0716-0.12580.06480.0220.028-22.864116.3433-5.0696
24.029-1.06110.19492.7425-0.01032.65180.02320.0416-0.1291-0.0934-0.09880.24660.2685-0.3584-0.01710.1556-0.0502-0.02350.1497-0.02390.19-13.1514-0.07811.1351
32.6043-0.5087-0.2282.47750.81812.50210.049-0.01170.0783-0.3855-0.11360.1505-0.2539-0.33410.00740.16280.0184-0.04090.1243-0.00630.1755-14.025110.2236-0.771
43.4610.38620.53711.7667-0.63252.5354-0.059-0.31770.0280.3163-0.11740.0340.0991-0.23930.15850.2374-0.00840.02290.1711-0.05530.167-5.49919.077222.149
54.9236-0.6746-1.86143.1856-0.0725.5491-0.1881-0.22950.14460.4477-0.03760.085-0.0377-0.17450.2330.1393-0.0272-0.00590.1283-0.01040.1189-4.023110.894120.6746
68.14061.28710.64413.07580.07617.1435-0.0189-0.25280.07030.1601-0.0673-0.6819-0.17910.4340.08610.211-0.0515-0.02390.14240.00080.26247.442817.593816.9327
72.88820.30810.67011.7797-0.64322.1670.0435-0.2795-0.10950.3089-0.0397-0.46790.25210.4954-0.02110.2210.065-0.08430.2810.00010.232411.05144.690422.9739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:42)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 43:97)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 98:150)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 151:196)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 197:211)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 212:231)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 232:277)

+
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