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- PDB-1ies: TETRAGONAL CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN -

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Basic information

Entry
Database: PDB / ID: 1ies
TitleTETRAGONAL CRYSTAL STRUCTURE OF NATIVE HORSE SPLEEN FERRITIN
ComponentsFERRITIN
KeywordsIRON STORAGE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 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: Acta Crystallogr.,Sect.D / Year: 1996
Title: Preliminary Results on X-Ray Diffraction Study of the Tetragonal Form of Native Horse Spleen Ferritin
Authors: Granier, T. / Gallois, B. / Dautant, A. / Langlois D'Estaintot, B. / 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.
#4: Journal: J.Mol.Biol. / Year: 1974
Title: A Tetragonal Crystal Form of Horse Spleen Apoferritin and its Relation to the Cubic Modification
Authors: Hoy, T.G. / Harrison, P.M. / Hoare, R.J.
History
DepositionMay 28, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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
B: FERRITIN
C: FERRITIN
D: FERRITIN
E: FERRITIN
F: FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,79711
Polymers119,2356
Non-polymers5625
Water4,900272
1
A: FERRITIN
B: FERRITIN
C: FERRITIN
D: FERRITIN
E: FERRITIN
F: FERRITIN
hetero molecules

A: FERRITIN
B: FERRITIN
C: FERRITIN
D: FERRITIN
E: FERRITIN
F: FERRITIN
hetero molecules

A: FERRITIN
B: FERRITIN
C: FERRITIN
D: FERRITIN
E: FERRITIN
F: FERRITIN
hetero molecules

A: FERRITIN
B: FERRITIN
C: FERRITIN
D: FERRITIN
E: FERRITIN
F: FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,18644
Polymers476,93824
Non-polymers2,24820
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area93690 Å2
ΔGint-332 kcal/mol
Surface area135440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.229, 147.229, 152.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11C-211-

HOH

21C-212-

HOH

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Components

#1: Protein
FERRITIN


Mass: 19872.428 Da / Num. of mol.: 6 / 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.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.4 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.66 Mammonium salfate1reservoir
280 mMcadmium sulfate1reservoir
33 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 51340 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 1.8 / % possible all: 60.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Observed criterion σ(I): 2 / Num. measured all: 354156

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR2.1refinement
XDSdata reduction
MARSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HRS

1hrs


Resolution: 2.6→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / σ(F): 1
Details: WARNING THE THREE C-TERMINAL RESIDUES 172 - 174, SIDE CHAIN ATOMS FOR RESIDUES SER 1, GLN 3, GLU 45, HIS 49, GLU 53, GLU 56, GLU 57, LYS 67, GLN 82, GLU 136, SER 157 AND GLN 158 ARE POORLY ...Details: WARNING THE THREE C-TERMINAL RESIDUES 172 - 174, SIDE CHAIN ATOMS FOR RESIDUES SER 1, GLN 3, GLU 45, HIS 49, GLU 53, GLU 56, GLU 57, LYS 67, GLN 82, 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
Rwork0.201 -
obs0.201 33428
Displacement parametersBiso mean: 25.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8388 0 5 272 8665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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: 2.6→2.66 Å
RfactorNum. reflection% reflection
Rwork0.28 933 -
obs--29 %
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_deg1.7
LS refinement shell
*PLUS
Lowest resolution: 2.7 Å / Rfactor Rwork: 0.27

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