[English] 日本語
Yorodumi
- PDB-2xv1: Crystal structure of the triscatecholate siderophore binding prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xv1
TitleCrystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis complexed with Ferric MECAM
ComponentsIRON-UPTAKE SYSTEM-BINDING PROTEIN
KeywordsTRANSPORT PROTEIN / HIGH AFFINITY IRON IMPORT / BACILLIBACTIN AND ENTEROBACTIN BINDING / IRON TRANSPORT
Function / homology
Function and homology information


iron ion transport / outer membrane-bounded periplasmic space / membrane raft / plasma membrane / cytoplasm
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ECA / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Iron-uptake system-binding protein
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPeuckert, F. / Miethke, M. / Schwoerer, C.J. / Albrecht, A.G. / Oberthuer, M. / Marahiel, M.A.
CitationJournal: Chem.Biol. / Year: 2011
Title: The Siderophore Binding Protein Feua Shows Limited Promiscuity Toward Exogenous Triscatecholates
Authors: Peuckert, F. / Ramos-Vega, A.L. / Miethke, M. / Schwoerer, C.J. / Albrecht, A.G. / Oberthuer, M. / Marahiel, M.A.
History
DepositionOct 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Dec 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IRON-UPTAKE SYSTEM-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7787
Polymers34,7471
Non-polymers1,0326
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.960, 63.440, 56.210
Angle α, β, γ (deg.)90.00, 110.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein IRON-UPTAKE SYSTEM-BINDING PROTEIN / SIDEROPHORE BINDING PROTEIN / TRISCATECHOLATE BINDING PROTEIN


Mass: 34746.660 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: ATCC 21332 / Plasmid: POK01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40409

-
Non-polymers , 5 types, 96 molecules

#2: Chemical ChemComp-ECA / N,N',N''-[BENZENE-1,3,5-TRIYLTRIS(METHYLENE)]TRIS(2,3-DIHYDROXYBENZAMIDE)


Mass: 573.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27N3O9
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE TWO DIFFERRENCES BETWEEN THE COORDINATE FILE AND AND THE UNIPROT SEQUENCE (T161 AND I218) ARE ...THE TWO DIFFERRENCES BETWEEN THE COORDINATE FILE AND AND THE UNIPROT SEQUENCE (T161 AND I218) ARE MENTIONED AS VARIANTS BY THE DEPOSITORS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.23 % / Description: NONE
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM 45% (V/V) PEG 300, 100 MM PHOSPHATE-CITRATE PH 5.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 9, 2010 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.15→40.55 Å / Num. obs: 13962 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 39.067 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WHY

2why


Resolution: 2.15→37.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.875 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23659 1206 8.6 %RANDOM
Rwork0.17812 ---
obs0.18312 12740 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.326 Å2
Baniso -1Baniso -2Baniso -3
1-3.11 Å20 Å22.11 Å2
2---3.12 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.15→37.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 67 90 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222262
X-RAY DIFFRACTIONr_bond_other_d0.0010.021494
X-RAY DIFFRACTIONr_angle_refined_deg1.1422.0043067
X-RAY DIFFRACTIONr_angle_other_deg0.833.0033683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1615284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67626.54884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17215393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.167153
X-RAY DIFFRACTIONr_chiral_restr0.0590.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
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_it0.3561.51420
X-RAY DIFFRACTIONr_mcbond_other0.0681.5563
X-RAY DIFFRACTIONr_mcangle_it0.64122290
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.033842
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6034.5776
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: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 80 -
Rwork0.305 972 -
obs--97.95 %
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)
12.0299-0.1578-0.29674.3149-0.27013.1563-0.10130.4343-0.0949-0.84140.09150.03120.1736-0.08560.00980.3455-0.05670.00960.2411-0.01780.101210.43985.96881.6163
23.4085-0.2862-4.38155.70433.36915.7953-0.01970.0701-0.4236-0.1860.01430.56360.1077-0.96670.00540.0982-0.066-0.11640.40760.0490.5455-6.0361.437116.6236
30.96190.1252-0.14554.04081.17242.3359-0.0177-0.00080.03480.2770.04090.070.0707-0.0796-0.02330.08550.0301-0.00440.15230.03860.15469.23716.358326.0033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 142
2X-RAY DIFFRACTION2A143 - 165
3X-RAY DIFFRACTION3A166 - 300

+
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