[English] 日本語
Yorodumi
- PDB-8sqr: Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sqr
TitleCrystal Structure of Bacterioferritin (Bfr) from Brucella abortus (iron bound, F16L mutant)
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
ACETATE ION / : / PROTOPORPHYRIN IX CONTAINING FE / Bacterioferritin
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus (iron bound, F16L mutant)
Authors: Lovell, S. / Liu, L. / Battaile, K.P.
History
DepositionMay 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,27616
Polymers18,8561
Non-polymers1,42015
Water2,198122
1
A: Bacterioferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)486,629384
Polymers452,54824
Non-polymers34,081360
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area121760 Å2
ΔGint-3352 kcal/mol
Surface area126680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.032, 113.032, 113.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-201-

MG

21A-204-

SO4

31A-204-

SO4

41A-205-

CL

51A-214-

HEM

61A-321-

HOH

71A-352-

HOH

81A-402-

HOH

91A-418-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Bacterioferritin


Mass: 18856.180 Da / Num. of mol.: 1 / Mutation: F16L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Gene: bfr, BAB2_0675 / Plasmid: BrabA.00028.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2YKI4, ferroxidase

-
Non-polymers , 8 types, 137 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 21% MPD, 0.4M MgCl2, 0.1M Ac pH 4.6, BrabA.00028.a.A1.PW39164 at 10 mg/mL. Plate: Liu-S-066, well G9, 2. Puck: PSL-1801, Cryo: 35% MPD + crystallant. 5 minute soak in 25 mM ferrous ammonium sulfate in cryo
PH range: '

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 14, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→46.15 Å / Num. obs: 30324 / % possible obs: 100 % / Redundancy: 58.1 % / CC1/2: 1 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.022 / Rrim(I) all: 0.168 / Χ2: 1 / Net I/σ(I): 22.8 / Num. measured all: 1761720
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 60.9 % / Rmerge(I) obs: 3.939 / Num. measured all: 95600 / Num. unique obs: 1571 / CC1/2: 0.728 / Rpim(I) all: 0.507 / Rrim(I) all: 3.972 / Χ2: 0.98 / Net I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→32.63 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 1488 4.91 %
Rwork0.1731 --
obs0.1738 30307 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 75 122 1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081424
X-RAY DIFFRACTIONf_angle_d0.9021946
X-RAY DIFFRACTIONf_dihedral_angle_d16.035530
X-RAY DIFFRACTIONf_chiral_restr0.041199
X-RAY DIFFRACTIONf_plane_restr0.008253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.29121200.26752572X-RAY DIFFRACTION100
1.7-1.760.24741450.25152558X-RAY DIFFRACTION100
1.76-1.830.24971240.21332562X-RAY DIFFRACTION100
1.84-1.920.21621410.19262566X-RAY DIFFRACTION100
1.92-2.020.1881440.18672578X-RAY DIFFRACTION100
2.02-2.150.20221350.17662562X-RAY DIFFRACTION100
2.15-2.310.19371290.15742617X-RAY DIFFRACTION100
2.31-2.540.17931340.15992608X-RAY DIFFRACTION100
2.54-2.910.161400.15822643X-RAY DIFFRACTION100
2.91-3.670.20261280.16172692X-RAY DIFFRACTION100
3.67-32.630.16471480.17262861X-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)
13.0961-4.4908-3.24737.77535.63854.3083-0.1505-0.0431-0.08420.25910.08270.20350.117-0.00890.1510.18440.0453-0.01650.17770.01610.146332.556530.27296.4817
22.2114-3.0724-2.10974.51163.79342.8206-0.0180.01510.02040.14770.00720.0084-0.04310.00270.01520.2111-0.00620.02280.1820.01940.186141.441526.271115.2952
31.8201-0.74161.11466.81782.50682.8605-0.17220.31780.0906-0.0756-0.06240.253-0.1057-0.15930.25660.1455-0.01360.03310.18460.01260.127343.98036.7031-2.0172
41.1392-3.2626-2.72398.14336.74365.59730.079-0.04560.0715-0.0477-0.0065-0.0877-0.14950.0149-0.10750.22910.02580.00890.196-0.00140.192738.269732.91426.9185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 35 )

+
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