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- PDB-1rci: BULLFROG RED CELL L FERRITIN TARTRATE/MG/PH 5.5 -

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Basic information

Entry
Database: PDB / ID: 1rci
TitleBULLFROG RED CELL L FERRITIN TARTRATE/MG/PH 5.5
ComponentsL FERRITIN
KeywordsIRON STORAGE
Function / homology
Function and homology information


ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / 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
TRIMETHYL GLYCINE / Ferritin, lower subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsTrikha, J. / Theil, E.C. / Allewell, N.M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: High resolution crystal structures of amphibian red-cell L ferritin: potential roles for structural plasticity and solvation in function.
Authors: Trikha, J. / Theil, E.C. / Allewell, N.M.
#1: Journal: Proteins / Year: 1994
Title: Crystallization and Structural Analysis of Bullfrog Red Cell L-Subunit Ferritins
Authors: Trikha, J. / Waldo, G.S. / Lewandowski, F.A. / Ha, Y. / Theil, E.C. / Weber, P.C. / Allewell, N.M.
History
DepositionAug 4, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1112
Polymers19,9921
Non-polymers1181
Water55831
1
A: L FERRITIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)482,65248
Polymers479,81724
Non-polymers2,83624
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 area95090 Å2
ΔGint-232 kcal/mol
Surface area126760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)181.446, 181.446, 181.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Atom site foot note1: CIS PROLINE - PRO 132

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Components

#1: Protein L FERRITIN


Mass: 19992.359 Da / Num. of mol.: 1 / Mutation: H25Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Cell: RED CELL / Gene: CDNA / Plasmid: PET 3A / Gene (production host): CDNA / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P07797
#2: Chemical ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
pH: 5.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mM11MgCl2
20.1 Msodium tartrate11
30.1 Msodium citrate11

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: NICOLET / Detector: AREA DETECTOR / Date: Jun 15, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 14234 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.124
Reflection
*PLUS
Rmerge(I) obs: 0.124

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 2
RfactorNum. reflection
Rfree0.274 -
Rwork0.186 -
obs0.186 14060
Displacement parametersBiso mean: 7.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 8 31 1430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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