[English] 日本語
Yorodumi
- PDB-6p8l: Escherichia coli Bacterioferritin Substituted with Zinc Protoporp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p8l
TitleEscherichia coli Bacterioferritin Substituted with Zinc Protoporphyrin IX (Zn Absorption Edge X-ray Data)
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / OXIDOREDUCTASE / bacterioferritin / zinc protoporphyrin IX / photosensitizer / ferritin
Function / homology
Function and homology information


iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MALONATE ION / PROTOPORPHYRIN IX CONTAINING ZN / Bacterioferritin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsTaylor, A.B. / Cioloboc, D. / Kurtz, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)8UL1TR001120 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction.
Authors: Benavides, B.S. / Valandro, S. / Cioloboc, D. / Taylor, A.B. / Schanze, K.S. / Kurtz Jr., D.M.
History
DepositionJun 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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 / pdbx_validate_chiral / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,70762
Polymers222,21612
Non-polymers7,49050
Water28,7341595
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,413124
Polymers444,43224
Non-polymers14,981100
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area104270 Å2
ΔGint-356 kcal/mol
Surface area127460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.918, 207.918, 143.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-202-

NA

21F-203-

NA

31C-331-

HOH

41F-417-

HOH

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Bacterioferritin / BFR / Cytochrome b-1 / Cytochrome b-557


Mass: 18518.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: bfr, b3336, JW3298 / Plasmid: pCV3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABD3, ferroxidase

-
Non-polymers , 5 types, 1645 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical
ChemComp-ZNH / PROTOPORPHYRIN IX CONTAINING ZN


Mass: 626.051 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32N4O4Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1595 / 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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.4 M sodium malonate, pH 6.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.2822
SYNCHROTRONAPS 24-ID-C21.319
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELFeb 2, 2018
DECTRIS PILATUS 6M-F2PIXELFeb 2, 2018
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryo-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Cryo-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.28221
21.3191
Reflection

Entry-ID: 6P8L / CC1/2: 0.998 / % possible obs: 99.8 %

Resolution (Å)Num. obsRedundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
2.1-92.651792577.330.160.1690.0670.18218.2
2.5-92.981079267.20.1770.0710.19128.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.1-2.217.51.7771.1258790.6990.9721.908199.9
2.5-2.647.21.7811.2155630.7370.7121.92299.8

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 6P8K

6p8k


Resolution: 2.1→92.65 Å / SU ML: 0.2974 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.7513
RfactorNum. reflection% reflection
Rfree0.2402 3852 1.12 %
Rwork0.2129 --
obs0.2132 344368 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→92.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15528 0 470 1598 17596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006816835
X-RAY DIFFRACTIONf_angle_d1.971822823
X-RAY DIFFRACTIONf_chiral_restr0.06222316
X-RAY DIFFRACTIONf_plane_restr0.0042974
X-RAY DIFFRACTIONf_dihedral_angle_d17.71056475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.40971280.352311354X-RAY DIFFRACTION92.76
2.13-2.160.411390.347612226X-RAY DIFFRACTION99.61
2.16-2.190.36471360.328312185X-RAY DIFFRACTION99.81
2.19-2.220.34841390.322612223X-RAY DIFFRACTION99.9
2.22-2.250.35441420.315112268X-RAY DIFFRACTION99.85
2.25-2.280.35941400.303912320X-RAY DIFFRACTION99.88
2.28-2.320.33421390.302712247X-RAY DIFFRACTION99.98
2.32-2.350.32791390.296412187X-RAY DIFFRACTION99.79
2.35-2.40.29231350.29412253X-RAY DIFFRACTION99.66
2.4-2.440.32311400.291412177X-RAY DIFFRACTION99.52
2.44-2.490.31981380.288512158X-RAY DIFFRACTION99.34
2.49-2.540.31521330.261512245X-RAY DIFFRACTION99.66
2.54-2.590.24851400.258412206X-RAY DIFFRACTION99.56
2.59-2.650.29941380.254712249X-RAY DIFFRACTION99.79
2.65-2.720.30851390.243812255X-RAY DIFFRACTION99.82
2.72-2.790.25621380.235212215X-RAY DIFFRACTION99.82
2.79-2.870.27071410.226712260X-RAY DIFFRACTION99.69
2.87-2.970.2691370.228212240X-RAY DIFFRACTION99.68
2.97-3.070.24461370.217612149X-RAY DIFFRACTION99.34
3.07-3.20.28121400.197112177X-RAY DIFFRACTION99.27
3.2-3.340.20641370.174512181X-RAY DIFFRACTION99.44
3.34-3.520.20591350.163712197X-RAY DIFFRACTION99.29
3.52-3.740.19921410.164812184X-RAY DIFFRACTION99.58
3.74-4.030.16981320.144912207X-RAY DIFFRACTION99.39
4.03-4.430.15341410.136112075X-RAY DIFFRACTION98.41
4.43-5.070.17891360.14312169X-RAY DIFFRACTION99.2
5.07-6.390.16571350.193612205X-RAY DIFFRACTION99.54
6.39-92.650.18351370.181411704X-RAY DIFFRACTION95.32

+
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