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- PDB-1dat: CUBIC CRYSTAL STRUCTURE RECOMBINANT HORSE L APOFERRITIN -

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Basic information

Entry
Database: PDB / ID: 1dat
TitleCUBIC CRYSTAL STRUCTURE RECOMBINANT HORSE L APOFERRITIN
ComponentsL FERRITIN
KeywordsIRON STORAGE / APOFERRITIN / LIGHT CHAIN
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: 2.05 Å
AuthorsGallois, B. / Granier, T. / Langlois D'Estaintot, B. / Crichton, R.R. / Roland, F.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 1997
Title: X-ray structure of recombinant horse L-chain apoferritin at 2.0 angstrom resolution: Implications for stability and function.
Authors: Gallois, B. / dEstaintot, B.L. / Michaux, M.A. / Dautant, A. / Granier, T. / Precigoux, G. / Soruco, J.A. / Roland, F. / ChavasAlba, O. / Herbas, A. / Crichton, R.R.
#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: Biochim.Biophys.Acta / Year: 1993
Title: Cloning, Expression and Characterization of Horse L-Ferritin in Escherichia Coli
Authors: Takeda, S. / Ohta, M. / Ebina, S. / Nagayama, K.
#3: Journal: FEBS Lett. / Year: 1981
Title: Amino Acid Sequence of Horse Spleen Apoferritin
Authors: Heusterspreute, M. / Crichton, R.R.
#4: 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
DepositionNov 14, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Refinement description
Category: pdbx_database_status / software ...pdbx_database_status / software / struct_conf / struct_conf_type
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_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_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

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Assembly

Deposited unit
A: L FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1944
Polymers19,8561
Non-polymers3373
Water1,910106
1
A: L FERRITIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)484,64796
Polymers476,55324
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 area93980 Å2
ΔGint-264 kcal/mol
Surface area137880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)183.700, 183.700, 183.700
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 L FERRITIN


Mass: 19856.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: CDNA / Organ: LIVER / Plasmid: BMH-71-18 / Gene (production host): CDNA / Production host: Escherichia coli (E. coli) / 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.: 106 / 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: 3.26 Å3/Da / Density % sol: 62.2 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
23 mM1dropNaN3
30.5 Mammonium sulfate1reservoir
40.04 Mcadmium sulfate1reservoir

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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 2, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 2.05→16.05 Å / Num. obs: 16993 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.096 / Net I/σ(I): 6.4
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.278 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 16931 / Num. measured all: 179720 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.278

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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: PDB ENTRY 1IER

1ier


Resolution: 2.05→8 Å / σ(F): 4
RfactorNum. reflection% reflection
Rwork0.178 --
obs0.178 13018 77.3 %
Displacement parametersBiso mean: 19.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 3 106 1506
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
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: 2.05→2.15 Å
RfactorNum. reflection% reflection
Rwork0.191 1104 -
obs--57.5 %
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.82
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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