[English] 日本語
Yorodumi
- PDB-6mfl: Structure of siderophore binding protein BauB bound to a complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mfl
TitleStructure of siderophore binding protein BauB bound to a complex between two molecules of acinetobactin and ferric iron.
ComponentsSiderophore Binding Protein BauB
KeywordsMETAL TRANSPORT / Siderophore Binding Protein / periplasmic protein / substrate binding protein / iron acquisition
Function / homology
Function and homology information


FatB domain / 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
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGulick, A.M. / Bailey, D.C. / Wencewicz, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI116998 United States
CitationJournal: Biochemistry / Year: 2018
Title: Crystal Structure of the Siderophore Binding Protein BauB Bound to an Unusual 2:1 Complex Between Acinetobactin and Ferric Iron.
Authors: Bailey, D.C. / Bohac, T.J. / Shapiro, J.A. / Giblin, D.E. / Wencewicz, T.A. / Gulick, A.M.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Revision 1.4May 1, 2024Group: Structure summary / Category: entity / Item: _entity.pdbx_description

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Siderophore Binding Protein BauB
B: Siderophore Binding Protein BauB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,14410
Polymers69,5232
Non-polymers1,6218
Water6,702372
1
A: Siderophore Binding Protein BauB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5725
Polymers34,7621
Non-polymers8114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Siderophore Binding Protein BauB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5725
Polymers34,7621
Non-polymers8114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.762, 137.055, 56.208
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Siderophore Binding Protein BauB / Probable ferric acinetobactin binding protein


Mass: 34761.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bauB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76HK0
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-OPV / ~{N}-[(4~{S},5~{S})-2-[2-(1~{H}-imidazol-4-yl)ethyl]-5-methyl-3-oxidanylidene-1,2-oxazolidin-4-yl]-2,3-bis(oxidanyl)benzamide


Mass: 346.338 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0941.21
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2871vapor diffusion, hanging drop625% PEG MME 5k, 50 mM MES
2872vapor diffusion, hanging drop834% PEG 4k, 100 mM EPPS

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11131
21131
31132
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.9795
SYNCHROTRONSSRL BL12-220.9795
SYNCHROTRONAPS 23-ID-D31.0332
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXEL
DECTRIS PILATUS3 6M2PIXELFeb 10, 2018
DECTRIS PILATUS3 6M3PIXELNov 12, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.03321
31
Reflection

Entry-ID: 6MFL

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.9-684458099.27.80.970.1780.0560.204111.6
1.9-6826033887.36.70.9950.090.0560.106211.8
1.99-45.63814997.73.20.9410.190.1434.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
1.9-26.40.576.7379280.9740.0760.204190.5
1.99-2.0430.5812.226100.4190.45291.1

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFV

3gfv


Resolution: 1.9→56.208 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 2140 4.84 %random
Rwork0.1694 ---
obs0.1715 44255 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→56.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 110 372 4904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114658
X-RAY DIFFRACTIONf_angle_d1.1186335
X-RAY DIFFRACTIONf_dihedral_angle_d17.1542787
X-RAY DIFFRACTIONf_chiral_restr0.069710
X-RAY DIFFRACTIONf_plane_restr0.007825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94420.21731300.16492785X-RAY DIFFRACTION96
1.9442-1.99280.24451430.16822751X-RAY DIFFRACTION97
1.9928-2.04670.22811740.16662698X-RAY DIFFRACTION97
2.0467-2.10690.22021400.18192789X-RAY DIFFRACTION98
2.1069-2.17490.21951630.16372780X-RAY DIFFRACTION99
2.1749-2.25270.2711510.16452815X-RAY DIFFRACTION99
2.2527-2.34290.18971330.15782837X-RAY DIFFRACTION99
2.3429-2.44950.20481510.16422775X-RAY DIFFRACTION99
2.4495-2.57860.20641350.16282800X-RAY DIFFRACTION98
2.5786-2.74020.23641340.16252852X-RAY DIFFRACTION100
2.7402-2.95180.20241350.17052863X-RAY DIFFRACTION100
2.9518-3.24880.26311390.18082812X-RAY DIFFRACTION99
3.2488-3.71880.18581360.16912865X-RAY DIFFRACTION100
3.7188-4.6850.1751370.15422851X-RAY DIFFRACTION99
4.685-56.23260.22191390.19682842X-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://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