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- PDB-1lb3: Structure of recombinant mouse L chain ferritin at 1.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 1lb3
TitleStructure of recombinant mouse L chain ferritin at 1.2 A resolution
ComponentsFERRITIN LIGHT CHAIN 1
KeywordsMETAL BINDING PROTEIN / IRON STORAGE
Function / homology
Function and homology information


: / autolysosome / intracellular sequestering of iron ion / endocytic vesicle lumen / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / extracellular region / identical protein 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 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsGranier, T. / Langlois D'Estaintot, B. / Gallois, B. / Chevalier, J.-M. / Precigoux, G. / Santambrogio, P. / Arosio, P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2003
Title: Structural description of the active sites of mouse L-chain ferritin at 1.2A resolution
Authors: Granier, T. / Langlois D'Estaintot, B. / Gallois, B. / Chevalier, J.-M. / Precigoux, G. / Santambrogio, P. / Arosio, P.
History
DepositionApr 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,05814
Polymers20,6701
Non-polymers1,38813
Water5,152286
1
A: FERRITIN LIGHT CHAIN 1
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)529,396336
Polymers496,08424
Non-polymers33,312312
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 area112710 Å2
ΔGint-703 kcal/mol
Surface area133060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)180.590, 180.590, 180.590
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-717-

CD

DetailsThe biological assembly is a 24mer. Coordinates for a complete multimer representing the known biologically significant oligomerization state of the molecule can be generated from the monomer in the assymmetric unit by the following symmetry operations: -X,-Y,Z; -X,Y,-Z; X,-Y,-Z; Z,X,Y; Z,-X,-Y; -Z,-X,Y; -Z,X,-Y; Y,Z,X; -Y,Z,-X; Y,-Z,-X; -Y,-Z,X; Y,X,-Z; -Y,-X,-Z; Y,-X,Z; -Y,X,Z; X,Z,-Y; -X,Z,Y; -X,-Z,-Y; X,-Z,Y; Z,Y,-X; Z,-Y,X; -Z,Y,X; -Z,-Y,-X;

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Components

#1: Protein FERRITIN LIGHT CHAIN 1 / / FERRITIN L SUBUNIT 1


Mass: 20670.164 Da / Num. of mol.: 1 / Mutation: T121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: FTL / Plasmid: pMLF27 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P29391
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN ENGINEERED MUTATION THR125ALA (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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulphate, cadmium sulphate, sodium azide, tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 293 K / Details: Granier, T., (2001) Acta Crystallogr., D57, 1491.
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: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.966 / Wavelength: 0.966 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2000 / Details: W/SI MIRRORS
RadiationMonochromator: Si (111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.21→14 Å / Num. all: 74509 / Num. obs: 74509 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.066 / Net I/σ(I): 6.4
Reflection shellResolution: 1.21→1.25 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 5144 / Rsym value: 0.48 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 14 Å / Num. measured all: 399787 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 98.4 % / Num. unique obs: 5144 / Rmerge(I) obs: 0.602

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXL-97model building
SHELXL-97refinement
CCP4(SCALA)data scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H96

1h96


Resolution: 1.21→14 Å / Num. parameters: 16266 / Num. restraintsaints: 16802 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1595 3747 5.3 %RANDOM
Rwork0.132 ---
all0.1335 74393 --
obs0.1335 74393 98.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 38 / Occupancy sum hydrogen: 1287.25 / Occupancy sum non hydrogen: 1622.33
Refinement stepCycle: LAST / Resolution: 1.21→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 31 286 1656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d1.69
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0223
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.028
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.087
LS refinement shellResolution: 1.21→1.26 Å
RfactorNum. reflection% reflection
Rfree0.222 363 -
Rwork0.2 --
obs-7467 89.7 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 14 Å / Rfactor all: 0.134 / Rfactor Rfree: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.69
LS refinement shell
*PLUS
Rfactor Rfree: 0.22 / Rfactor Rwork: 0.2

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