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- PDB-6tr9: Crystal structure of human L ferritin (HuLf) triple variant E60A-... -

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Basic information

Entry
Database: PDB / ID: 6tr9
TitleCrystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / human L ferritin / HuLf / E60A-E61A-E64A
Function / homology
Function and homology information


ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / autolysosome / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport ...ferritin complex / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / autolysosome / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport / intracellular iron ion homeostasis / iron ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / cytosol / 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
: / Ferritin light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 18, 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.ptnr1_symmetry / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6618
Polymers19,8751
Non-polymers7877
Water1,964109
1
AAA: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)495,875192
Polymers476,99024
Non-polymers18,885168
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 area101520 Å2
ΔGint-927 kcal/mol
Surface area141260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.215, 151.215, 151.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11AAA-201-

CD

21AAA-204-

CD

31AAA-376-

HOH

41AAA-406-

HOH

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Components

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19874.572 Da / Num. of mol.: 1 / Mutation: E60A,E61A,E64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTL / Plasmid: pET-21c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pLysS / References: UniProt: P02792
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.46→75.61 Å / Num. obs: 11055 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.2 % / Biso Wilson estimate: 50.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.024 / Rrim(I) all: 0.112 / Net I/σ(I): 21.2
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1562 / CC1/2: 0.929 / Rpim(I) all: 0.233 / Rrim(I) all: 1.09 / % 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: 5LG8

5lg8


Resolution: 2.46→61.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.246
RfactorNum. reflection% reflection
Rfree0.2579 581 5.318 %
Rwork0.2005 --
all0.204 --
obs-10926 98.869 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.624 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.46→61.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 7 109 1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131398
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171286
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.6381886
X-RAY DIFFRACTIONr_angle_other_deg2.4651.5772973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27122.22281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80715245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0511510
X-RAY DIFFRACTIONr_chiral_restr0.1880.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021584
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02306
X-RAY DIFFRACTIONr_nbd_refined0.2290.2319
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.21108
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2680
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.254
X-RAY DIFFRACTIONr_metal_ion_refined0.2450.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.212
X-RAY DIFFRACTIONr_nbd_other0.2080.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2240.26
X-RAY DIFFRACTIONr_mcbond_it4.355.013689
X-RAY DIFFRACTIONr_mcbond_other4.3395.008688
X-RAY DIFFRACTIONr_mcangle_it6.1487.487860
X-RAY DIFFRACTIONr_mcangle_other6.1527.494861
X-RAY DIFFRACTIONr_scbond_it5.8345.345708
X-RAY DIFFRACTIONr_scbond_other5.835.35709
X-RAY DIFFRACTIONr_scangle_it8.2377.8261025
X-RAY DIFFRACTIONr_scangle_other8.2347.8311026
X-RAY DIFFRACTIONr_lrange_it9.87658.3811607
X-RAY DIFFRACTIONr_lrange_other9.81958.0761590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.5240.373450.284753X-RAY DIFFRACTION99.75
2.524-2.5930.364340.279714X-RAY DIFFRACTION98.9418
2.593-2.6680.347460.263719X-RAY DIFFRACTION99.2218
2.668-2.750.471230.266702X-RAY DIFFRACTION98.7738
2.75-2.8410.329260.247689X-RAY DIFFRACTION98.7569
2.841-2.940.273370.242635X-RAY DIFFRACTION98.6784
2.94-3.0510.289390.234617X-RAY DIFFRACTION98.7952
3.051-3.1750.325340.237603X-RAY DIFFRACTION98.151
3.175-3.3170.274380.212568X-RAY DIFFRACTION98.0583
3.317-3.4780.248310.184556X-RAY DIFFRACTION98.1605
3.478-3.6660.229240.185537X-RAY DIFFRACTION97.7352
3.666-3.8880.239390.176498X-RAY DIFFRACTION98.895
3.888-4.1560.244300.173464X-RAY DIFFRACTION97.6285
4.156-4.4890.366220.159451X-RAY DIFFRACTION98.954
4.489-4.9160.167220.138433X-RAY DIFFRACTION100
4.916-5.4950.265200.157379X-RAY DIFFRACTION99.5012
5.495-6.3430.214250.195339X-RAY DIFFRACTION100
6.343-7.7610.271160.213299X-RAY DIFFRACTION100
7.761-10.9470.188240.155235X-RAY DIFFRACTION100

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