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- PDB-6tsx: Crystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 3... -

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Basic information

Entry
Database: PDB / ID: 6tsx
TitleCrystal structure of horse L ferritin (HoLf) Fe(III)-loaded for 30 minutes
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / horse L ferritin / HoLf / Fe(III) / trinuclear Fe(III) cluster
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / 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: 2.021 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 21, 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 / struct_conn_type
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.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.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

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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)21,12922
Polymers20,0801
Non-polymers1,05021
Water1,76598
1
AAA: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)507,103528
Polymers481,91424
Non-polymers25,189504
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 area94300 Å2
ΔGint-338 kcal/mol
Surface area135910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.242, 181.242, 181.242
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-215-

CD

21AAA-216-

FE

31AAA-304-

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, 119 molecules

#2: Chemical
ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 15 / 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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30 mM cadmium nitrate, 1 M ammonium sulfate, 200 mM sodium acetate, pH 5.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.9795
SYNCHROTRONDiamond I0421.73894
SYNCHROTRONDiamond I0431.7512
Detector
TypeIDDetectorDate
DECTRIS EIGER2 X 16M1PIXELJul 26, 2019
DECTRIS EIGER2 X 16M2PIXELJul 26, 2019
DECTRIS EIGER2 X 16M3PIXELJul 26, 2019
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)MADMx-ray2
3Si(111)MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.738941
31.75121
Reflection

Entry-ID: 6TSX / Observed criterion σ(I): 2 / % possible obs: 100 %

Resolution (Å)Num. obsRedundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
2.02-104.641729821.738.710.0560.0130.06130.4
2.3-104.641187417.952.80.9990.0680.0190.084223.8
2.3-90.471183017.754.90.9990.0790.020.085317.9
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID
2.02-2.1322.20.9013.924420.9150.1990.9411
2.3-2.42121.1492.116700.6850.3541.2432
2.3-2.4211.30.9572.316950.7490.3051.0413

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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: 2.021→54.706 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.136
RfactorNum. reflection% reflection
Rfree0.2211 900 5.204 %
Rwork0.1844 --
all0.186 --
obs-17294 99.971 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.696 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.021→54.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 21 98 1467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131379
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171275
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.6361859
X-RAY DIFFRACTIONr_angle_other_deg2.41.5752943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.165170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85322.38184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59915241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8351511
X-RAY DIFFRACTIONr_chiral_restr0.1320.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021563
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02302
X-RAY DIFFRACTIONr_nbd_refined0.2460.2315
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.21035
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2682
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.252
X-RAY DIFFRACTIONr_metal_ion_refined0.150.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.210
X-RAY DIFFRACTIONr_nbd_other0.1840.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.213
X-RAY DIFFRACTIONr_mcbond_it3.4744.185677
X-RAY DIFFRACTIONr_mcbond_other3.4774.184676
X-RAY DIFFRACTIONr_mcangle_it4.2116.245845
X-RAY DIFFRACTIONr_mcangle_other4.2086.247846
X-RAY DIFFRACTIONr_scbond_it6.4664.757701
X-RAY DIFFRACTIONr_scbond_other6.4624.755702
X-RAY DIFFRACTIONr_scangle_it9.1896.8671012
X-RAY DIFFRACTIONr_scangle_other9.1846.8651013
X-RAY DIFFRACTIONr_lrange_it10.18350.9511594
X-RAY DIFFRACTIONr_lrange_other9.86650.6411577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.021-2.0730.234670.2231182X-RAY DIFFRACTION100
2.073-2.130.177680.2091146X-RAY DIFFRACTION100
2.13-2.1920.213670.1931101X-RAY DIFFRACTION100
2.192-2.2590.194540.1871108X-RAY DIFFRACTION100
2.259-2.3330.211530.1841068X-RAY DIFFRACTION100
2.333-2.4150.213500.1641029X-RAY DIFFRACTION100
2.415-2.5060.197470.175985X-RAY DIFFRACTION100
2.506-2.6090.199460.167968X-RAY DIFFRACTION100
2.609-2.7240.21570.168917X-RAY DIFFRACTION100
2.724-2.8570.286540.161878X-RAY DIFFRACTION100
2.857-3.0120.203510.152834X-RAY DIFFRACTION100
3.012-3.1940.188490.157799X-RAY DIFFRACTION100
3.194-3.4150.156400.164770X-RAY DIFFRACTION100
3.415-3.6880.202370.151706X-RAY DIFFRACTION100
3.688-4.0390.209490.153652X-RAY DIFFRACTION100
4.039-4.5150.22320.157598X-RAY DIFFRACTION100
4.515-5.2120.265240.158552X-RAY DIFFRACTION100
5.212-6.380.391220.255474X-RAY DIFFRACTION100
6.38-9.0050.208210.25379X-RAY DIFFRACTION100

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