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- PDB-1h96: recombinant mouse L-chain ferritin -

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Basic information

Entry
Database: PDB / ID: 1h96
Titlerecombinant mouse L-chain ferritin
ComponentsFERRITIN LIGHT CHAIN 1
KeywordsIRON STORAGE
Function / homology
Function and homology information


ferritin complex / autolysosome / intracellular sequestering of iron ion / endocytic vesicle lumen / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / extracellular region / 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 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGranier, T. / Gallois, B. / D'Estaintot, B.L. / Dautant, A. / Chevalier, J.M. / Mellado, J.M. / Beaumont, C. / Santambrogio, P. / Arosio, P. / Precigoux, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Mouse L-Chain Ferritin at 1.6 A Resolution
Authors: Granier, T. / Gallois, B. / D'Estaintot, B.L. / Dautant, A. / Chevalier, J.M. / Mellado, J.M. / Beaumont, C. / Santambrogio, P. / Arosio, P. / Precigoux, G.
History
DepositionFeb 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / diffrn_source / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _diffrn_source.pdbx_synchrotron_y_n / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRITIN LIGHT CHAIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,77811
Polymers20,6701
Non-polymers1,10810
Water5,278293
1
A: FERRITIN LIGHT CHAIN 1
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)522,670264
Polymers496,08424
Non-polymers26,586240
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation24_555-z,-y,-x1
crystal symmetry operation14_555-y,-x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)180.820, 180.820, 180.820
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-489-

CD

21A-2162-

HOH

31A-2241-

HOH

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Components

#1: Protein FERRITIN LIGHT CHAIN 1


Mass: 20670.164 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse)
Description: FOR DETAILS SEE BEAUMONT, C., DUGAST, I., RENAUDIE, F., SOUROUJON, M., GRANDCHAMP, B. J. BIOL. CHEM., 1989, VOL. 264, 13, PP 7498-7504
Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / References: UniProt: P29391
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION THR121ALA (PCR ERROR)

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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: 2.6 Å3/Da / Density % sol: 52.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: HANGING DROP VAPOR DIFFUSION: DROPS MADE UP OF 3MICROL OF PROTEIN (3.5 MG/ML) IN 20 MM TRIS PH 7.4 AND 3 MICROL OF PRECIPITANT SOLUTION COMPOSED OF 0.92 M AMMONIUM SULFATE, 0.4% CDSO4 AND 3 MM NAN3
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13.5 mg/mlprotein1drop
220 mMTris1droppH7.4
30.92 Mammonium sulfate1reservoir
40.4 %1reservoirCdSO4
53 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 32400 / % possible obs: 95.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 11.83 Å2 / Rsym value: 0.071 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.38 / % possible all: 83.8
Reflection
*PLUS
Num. obs: 32292 / Num. measured all: 158991 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 83.8 % / Num. unique obs: 2042 / Num. measured obs: 8894 / Rmerge(I) obs: 0.38

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 1.6→14 Å / SU B: 1.2 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.075
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1637 5 %RANDOM
Rwork0.16 ---
obs-32339 95.7 %-
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 14 293 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.853
X-RAY DIFFRACTIONp_mcangle_it2.255.5
X-RAY DIFFRACTIONp_scbond_it3.54
X-RAY DIFFRACTIONp_scangle_it4.76.5
X-RAY DIFFRACTIONp_plane_restr0.0190.03
X-RAY DIFFRACTIONp_chiral_restr0.0960.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.5
X-RAY DIFFRACTIONp_multtor_nbd0.2850.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.5
X-RAY DIFFRACTIONp_xyhbond_nbd0.110.5
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor13.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19 Å / Rfactor obs: 0.16 / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å / Rfactor Rfree: 0.27 / Rfactor obs: 0.22

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