[English] 日本語
Yorodumi
- PDB-8ebg: Crystal structure of the probable FhuD FeIII-dicitrate-binding do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ebg
TitleCrystal structure of the probable FhuD FeIII-dicitrate-binding domain protein FecB from Mycobacterium tuberculosis
ComponentsFEIII-dicitrate-binding periplasmic lipoprotein FecB
KeywordsUNKNOWN FUNCTION / siderophore binding protein / siderophore / Structural Genomics / Midwest Center for Structural Genomics / MCSG / Metal binding protein / PSI-Biology
Function / homologyABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / outer membrane-bounded periplasmic space / extracellular region / plasma membrane / ACETIC ACID / FORMIC ACID / Probable FEIII-dicitrate-binding periplasmic lipoprotein FecB
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 Å
AuthorsCuff, M. / Kim, Y. / Endres, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of the probable FhuD FeIII-dicitrate-binding domain protein FecB from Mycobacterium tuberculosis
Authors: Cuff, M. / Kim, Y. / Endres, M. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FEIII-dicitrate-binding periplasmic lipoprotein FecB
B: FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4877
Polymers70,1052
Non-polymers3825
Water12,881715
1
A: FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1913
Polymers35,0521
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FEIII-dicitrate-binding periplasmic lipoprotein FecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2974
Polymers35,0521
Non-polymers2443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.631, 76.517, 79.076
Angle α, β, γ (deg.)90.000, 102.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein FEIII-dicitrate-binding periplasmic lipoprotein FecB


Mass: 35052.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: fecB, Rv3044 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: O53291
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M Ammonium acetate, 0.085 M sodium citrate pH 5.6, 25.5 % (w/v) PEG4000, 15 % glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 116192 / % possible obs: 95.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.06 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.058 / Net I/σ(I): 28.9
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2 / Num. unique obs: 4188 / CC1/2: 0.753 / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / % possible all: 69.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.43→28.85 Å / SU ML: 0.121 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.8335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1704 5643 4.86 %
Rwork0.1414 110498 -
obs0.1428 116141 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.04 Å2
Refinement stepCycle: LAST / Resolution: 1.43→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 25 715 5426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00885129
X-RAY DIFFRACTIONf_angle_d0.97117069
X-RAY DIFFRACTIONf_chiral_restr0.0867804
X-RAY DIFFRACTIONf_plane_restr0.0093975
X-RAY DIFFRACTIONf_dihedral_angle_d11.64861844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.440.25911130.21672615X-RAY DIFFRACTION66.49
1.44-1.460.22751430.19782822X-RAY DIFFRACTION74.2
1.46-1.480.26081540.18763149X-RAY DIFFRACTION82.31
1.48-1.50.20621790.17183488X-RAY DIFFRACTION90.08
1.5-1.520.191920.15733562X-RAY DIFFRACTION93.43
1.52-1.540.18641960.1453639X-RAY DIFFRACTION94.6
1.54-1.560.19532040.14173696X-RAY DIFFRACTION95.75
1.56-1.580.1711960.14183661X-RAY DIFFRACTION95.71
1.58-1.610.20261960.13653711X-RAY DIFFRACTION96.49
1.61-1.640.16981870.12943713X-RAY DIFFRACTION97.14
1.64-1.660.19841920.12343779X-RAY DIFFRACTION96.88
1.66-1.690.16811920.12053750X-RAY DIFFRACTION98.26
1.69-1.730.16612030.11353754X-RAY DIFFRACTION97.63
1.73-1.760.15921930.11133796X-RAY DIFFRACTION98.45
1.76-1.80.16041790.11553800X-RAY DIFFRACTION98.3
1.8-1.840.16342000.12383792X-RAY DIFFRACTION98.25
1.84-1.890.15562180.1323783X-RAY DIFFRACTION98.62
1.89-1.940.15271970.12893801X-RAY DIFFRACTION99.35
1.94-20.16191860.12613833X-RAY DIFFRACTION98.99
2-2.060.1681840.13213841X-RAY DIFFRACTION99.24
2.06-2.130.16551760.13273863X-RAY DIFFRACTION99.34
2.13-2.220.15182040.1283812X-RAY DIFFRACTION99.41
2.22-2.320.19121810.13413893X-RAY DIFFRACTION99.56
2.32-2.440.1561870.13593848X-RAY DIFFRACTION99.61
2.44-2.60.1771800.14643866X-RAY DIFFRACTION99.7
2.6-2.80.17211940.15083892X-RAY DIFFRACTION99.85
2.8-3.080.1782050.1573863X-RAY DIFFRACTION99.75
3.08-3.520.18252230.15513868X-RAY DIFFRACTION99.83
3.52-4.430.15041840.13993856X-RAY DIFFRACTION98.56
4.43-28.850.16592050.15073752X-RAY DIFFRACTION94.78

+
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