[English] 日本語
Yorodumi
- PDB-6i9t: Two minutes iron loaded Rana Catesbeiana H' ferritin variant H54N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i9t
TitleTwo minutes iron loaded Rana Catesbeiana H' ferritin variant H54N
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / Rana Catesbeiana H' ferritin / ferroxidase process / H54N variant / two minutes iron loaded / time-controlled iron loading
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / 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
: / Ferritin, middle subunit
Similarity search - Component
Biological speciesLithobates catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPozzi, C. / Di Pisa, F. / Mangani, S.
CitationJournal: J.Inorg.Biochem. / Year: 2019
Title: Effect of the point mutation H54N on the ferroxidase process of Rana catesbeiana H' ferritin.
Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Turano, P. / Mangani, S.
History
DepositionNov 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,26623
Polymers20,5991
Non-polymers66722
Water6,612367
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)510,377552
Polymers494,37924
Non-polymers15,998528
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_455-x-1,z,y1
crystal symmetry operation19_455-x-1,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation58_454-y-1/2,z,-x-1/21
crystal symmetry operation59_454y-1/2,-z,-x-1/21
crystal symmetry operation60_455-y-1/2,-z,x+1/21
crystal symmetry operation69_454z-1/2,y,-x-1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_455-z-1/2,y,x+1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation78_445z-1/2,-x-1/2,-y1
crystal symmetry operation79_445-z-1/2,-x-1/2,y1
crystal symmetry operation80_455-z-1/2,x+1/2,-y1
crystal symmetry operation85_455y-1/2,x+1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_445y-1/2,-x-1/2,z1
crystal symmetry operation88_455-y-1/2,x+1/2,z1
Buried area95430 Å2
ΔGint-680 kcal/mol
Surface area135900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.830, 183.830, 183.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-207-

MG

21A-208-

MG

31A-214-

CL

41A-215-

CL

51A-617-

HOH

61A-663-

HOH

-
Components

#1: Protein Ferritin, middle subunit / Ferritin M / Ferritin H' / Ferritin X


Mass: 20599.137 Da / Num. of mol.: 1 / Mutation: H54N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lithobates catesbeiana (American bullfrog)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P07798, ferroxidase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 8-9

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.95372
SYNCHROTRONELETTRA 5.2R21.73893
SYNCHROTRONELETTRA 5.2R31.76116
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDOct 8, 2012
DECTRIS PILATUS 2M2PIXELOct 29, 2012
DECTRIS PILATUS 2M3PIXELOct 29, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
3Si(111)SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
21.738931
31.761161
Reflection

Biso Wilson estimate: 5.67 Å2 / Entry-ID: 6I9T / Observed criterion σ(I): 2

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.2-22.468046697.210.80.9990.0580.0180.063119.2
1.7-42.262897796.79.90.9990.0590.020.066223.7
1.85-46.052319499.17.50.9960.0990.040.113313.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
1.2-1.265.60.3664110660.860.1880.452192.9
1.7-1.792.50.2323.133470.8730.1730.315279
1.85-1.955.60.7372.131650.6530.3470.854395.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LQH

4lqh


Resolution: 1.2→22.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.723 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.028 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13706 4142 5.1 %RANDOM
Rwork0.12074 ---
obs0.12158 76291 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.779 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.115 Å
Refinement stepCycle: 1 / Resolution: 1.2→22.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 22 367 1807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171499
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.6442280
X-RAY DIFFRACTIONr_angle_other_deg1.6421.5873531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9555227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67823.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9821511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021957
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
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_it0.792777
X-RAY DIFFRACTIONr_mcbond_other0.787776
X-RAY DIFFRACTIONr_mcangle_it1.042988
X-RAY DIFFRACTIONr_mcangle_other1.042989
X-RAY DIFFRACTIONr_scbond_it1.074887
X-RAY DIFFRACTIONr_scbond_other1.074887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5061269
X-RAY DIFFRACTIONr_long_range_B_refined2.7442118
X-RAY DIFFRACTIONr_long_range_B_other1.7032018
X-RAY DIFFRACTIONr_rigid_bond_restr1.46431189
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 278 -
Rwork0.204 5316 -
obs--92.62 %

+
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