[English] 日本語
Yorodumi
- PDB-3rav: Horse spleen apo-ferritin with bound Pentobarbital -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rav
TitleHorse spleen apo-ferritin with bound Pentobarbital
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / 4-HELIX BUNDLE / IRON / IRON STORAGE / METAL-BINDING
Function / homology
Function and homology information


: / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / 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, core subunit, four-helix bundle / Ferritin / 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
: / Chem-RAV / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 1.9 Å
AuthorsOakley, S.H. / Vedula, L.S. / Xi, J. / Liu, R. / Eckenhoff, R.G. / Loll, P.J.
CitationJournal: to be published
Title: High resolution view of barbiturate recognition by a protein binding site
Authors: Oakley, S.H. / Vedula, L.S. / Xi, J. / Liu, R. / Eckenhoff, R.G. / Loll, P.J.
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 11, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] ..._pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,96510
Polymers19,8721
Non-polymers1,0939
Water3,531196
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)503,167240
Polymers476,93824
Non-polymers26,229216
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 area99270 Å2
ΔGint-879 kcal/mol
Surface area134620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.480, 182.480, 182.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-175-

CD

21A-183-

RAV

31A-183-

RAV

-
Components

#1: Protein Ferritin light chain / / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: Spleen / References: UniProt: P02791
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-RAV / 5-ethyl-5-[(2S)-pentan-2-yl]pyrimidine-2,4,6(1H,3H,5H)-trione / Pentobarbital / Pentobarbital


Mass: 226.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.3 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2-1.6 M (NH4)2SO4 and 0.1-0.275 M CdSO4, 0.5 mM thiopental were mixed with equal volumes of apoferritin solution and equilibrated over 0.7-1 mL, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9774 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→45.62 Å / Num. all: 21095 / Num. obs: 21095 / % possible obs: 100 % / Observed criterion σ(F): 38.9 / Observed criterion σ(I): 7.8 / Redundancy: 34.09 % / Biso Wilson estimate: 21.63 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 34.09 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 7.8 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.62 Å
Translation2.5 Å45.62 Å

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Resolution: 1.9→45.62 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.2 / σ(F): 0.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1994 5.15 %RANDOM
Rwork0.174 ---
all0.176 21101 --
obs0.176 21072 99.9 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.874 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 75.75 Å2 / Biso mean: 22.472 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 32 196 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071461
X-RAY DIFFRACTIONf_angle_d0.9591981
X-RAY DIFFRACTIONf_chiral_restr0.065218
X-RAY DIFFRACTIONf_plane_restr0.003253
X-RAY DIFFRACTIONf_dihedral_angle_d15.726555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9470.2621160.2332605272199
1.947-20.2451690.20626022771100
2-2.0590.2261580.18626082766100
2.059-2.1250.1821270.17626572784100
2.125-2.2010.2271540.16225882742100
2.201-2.290.2011680.16625972765100
2.29-2.3940.2071530.1726082761100
2.394-2.520.2481250.16626152740100
2.52-2.6780.1741570.16226332790100
2.678-2.8850.2011440.15926252769100
2.885-3.1750.2361470.16126012748100
3.175-3.6340.2091200.15926542774100
3.634-4.5780.1791090.16126692778100
4.578-45.6330.21470.20926402787100

+
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