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- PDB-6trz: Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 1... -

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Basic information

Entry
Database: PDB / ID: 6trz
TitleCrystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 15 minutes
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / horse L ferritin / HoLf / Fe(III) / trinuclear Fe(III) cluster
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 / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / : / OXYGEN ATOM / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPozzi, C. / Ciambellotti, S. / Turano, P. / Mangani, S.
CitationJournal: Chemistry / Year: 2020
Title: Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin.
Authors: Ciambellotti, S. / Pozzi, C. / Mangani, S. / Turano, P.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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_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.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.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.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_symmetry
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,57910
Polymers20,0801
Non-polymers4999
Water2,828157
1
AAA: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)493,888240
Polymers481,91424
Non-polymers11,974216
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 area95050 Å2
ΔGint-470 kcal/mol
Surface area134120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.471, 180.471, 180.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11AAA-206-

FE

21AAA-208-

CD

31AAA-452-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 20079.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791

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Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30 mM cadmium nitrate, 1 M ammonium sulfate, and 200 mM sodium acetate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→90.23 Å / Num. obs: 17109 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.6 % / Biso Wilson estimate: 33.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.02 / Rrim(I) all: 0.094 / Net I/σ(I): 19.8
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 22 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2448 / CC1/2: 0.908 / Rpim(I) all: 0.194 / Rrim(I) all: 0.914 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LG2

5lg2


Resolution: 2.02→63.888 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.119
RfactorNum. reflection% reflection
Rfree0.1878 891 5.208 %
Rwork0.1648 --
all0.166 --
obs-17108 99.982 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.92 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.02→63.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 9 157 1521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131404
X-RAY DIFFRACTIONr_bond_other_d0.0350.0171301
X-RAY DIFFRACTIONr_angle_refined_deg1.991.6361895
X-RAY DIFFRACTIONr_angle_other_deg2.4311.5773001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46821.70588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61715249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.051513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021598
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02317
X-RAY DIFFRACTIONr_nbd_refined0.2470.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21091
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2685
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.286
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.214
X-RAY DIFFRACTIONr_nbd_other0.2090.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.222
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0190.21
X-RAY DIFFRACTIONr_mcbond_it3.2593.707685
X-RAY DIFFRACTIONr_mcbond_other3.263.706684
X-RAY DIFFRACTIONr_mcangle_it4.1735.525856
X-RAY DIFFRACTIONr_mcangle_other4.1715.526857
X-RAY DIFFRACTIONr_scbond_it5.5344.166717
X-RAY DIFFRACTIONr_scbond_other5.534.165718
X-RAY DIFFRACTIONr_scangle_it7.7386.0231036
X-RAY DIFFRACTIONr_scangle_other7.7346.0221037
X-RAY DIFFRACTIONr_lrange_it8.84844.91664
X-RAY DIFFRACTIONr_lrange_other8.77544.5021641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.0730.21710.2081173X-RAY DIFFRACTION100
2.073-2.1290.207660.1971138X-RAY DIFFRACTION100
2.129-2.1910.232660.191095X-RAY DIFFRACTION99.9139
2.191-2.2590.169520.1741080X-RAY DIFFRACTION100
2.259-2.3330.176500.1541051X-RAY DIFFRACTION100
2.333-2.4140.16520.1551020X-RAY DIFFRACTION100
2.414-2.5060.233470.16993X-RAY DIFFRACTION100
2.506-2.6080.229420.17942X-RAY DIFFRACTION100
2.608-2.7240.193640.16910X-RAY DIFFRACTION100
2.724-2.8570.192470.147874X-RAY DIFFRACTION100
2.857-3.0110.212510.143826X-RAY DIFFRACTION100
3.011-3.1930.17490.144792X-RAY DIFFRACTION100
3.193-3.4140.165380.146750X-RAY DIFFRACTION100
3.414-3.6870.171410.14699X-RAY DIFFRACTION100
3.687-4.0380.174450.132640X-RAY DIFFRACTION100
4.038-4.5140.209320.133602X-RAY DIFFRACTION100
4.514-5.2110.16240.134538X-RAY DIFFRACTION100
5.211-6.3780.198210.213474X-RAY DIFFRACTION100
6.378-9.0030.158220.207373X-RAY DIFFRACTION100

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