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- PDB-1ier: CUBIC CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN -

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Basic information

Entry
Database: PDB / ID: 1ier
TitleCUBIC CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN
ComponentsFERRITIN
KeywordsIRON STORAGE / FERRITIN / APOFERRITIN
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / 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
: / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 Å
AuthorsGranier, T. / Gallois, B. / Dautant, A. / Langlois D'Estaintot, B. / Precigoux, G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Comparison of the structures of the cubic and tetragonal forms of horse-spleen apoferritin.
Authors: Granier, T. / Gallois, B. / Dautant, A. / Langlois d'Estaintot, B. / Precigoux, G.
#1: Journal: Proteins / Year: 1996
Title: Structural Investigation of the Complexation Properties between Horse Spleen Apoferritin and Metalloporphyrins
Authors: Michaux, M.A. / Dautant, A. / Gallois, B. / Granier, T. / D'Estaintot, B.L. / Precigoux, G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: A Crystallographic Study of Haem Binding to Ferritin
Authors: Precigoux, G. / Yariv, J. / Gallois, B. / Dautant, A. / Courseille, C. / Langlois D'Estaintot, B.
#3: Journal: Nature / Year: 1980
Title: Helix Packing and Subunit Conformation in Horse Spleen Apoferritin
Authors: Clegg, G.A. / Stansfield, R.F. / Bourne, P.E. / Harrison, P.M.
History
DepositionMay 28, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 27, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / software / struct_conn
Item: _pdbx_database_status.process_site / _software.name
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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_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.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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2104
Polymers19,8721
Non-polymers3373
Water1,964109
1
A: FERRITIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)485,03296
Polymers476,93824
Non-polymers8,09472
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 area96320 Å2
ΔGint-329 kcal/mol
Surface area133720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)182.900, 182.900, 182.900
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-201-

CD

21A-202-

CD

31A-203-

CD

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Components

#1: Protein FERRITIN


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


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium salfate1reservoir
280 mMcadmium sulfate1reservoir
33 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 2.26→19.96 Å / Num. obs: 12699 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rsym value: 0.11 / Net I/σ(I): 6.5
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.414 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. measured all: 88762 / Rmerge(I) obs: 0.11

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Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR2.1phasing
RefinementStarting model: 1HRS

1hrs


Resolution: 2.26→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
Details: THE THREE C-TERMINAL RESIDUES 172 - 174, SIDE CHAIN ATOMS FOR RESIDUES SER 1, GLU 45, GLU 53, GLU 56, GLU 57, ARG 64, LYS 67, SER 131, GLU 136, SER 157 AND GLN 158 ARE POORLY DEFINED IN THE ...Details: THE THREE C-TERMINAL RESIDUES 172 - 174, SIDE CHAIN ATOMS FOR RESIDUES SER 1, GLU 45, GLU 53, GLU 56, GLU 57, ARG 64, LYS 67, SER 131, GLU 136, SER 157 AND GLN 158 ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP, PROBABLY BECAUSE OF DISORDER. ALL THE REMAINING RESIDUES HAVE WELL DEFINED DENSITY.
RfactorNum. reflection% reflection
Rwork0.187 --
obs0.187 11870 94.8 %
Displacement parametersBiso mean: 24.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.26→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 3 109 1510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.2
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
LS refinement shellResolution: 2.26→2.31 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rwork0.25 772 -
obs--94.1 %
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.6
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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