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- PDB-1fha: SOLVING THE STRUCTURE OF HUMAN H FERRITIN BY GENETICALLY ENGINEER... -

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Basic information

Entry
Database: PDB / ID: 1fha
TitleSOLVING THE STRUCTURE OF HUMAN H FERRITIN BY GENETICALLY ENGINEERING INTERMOLECULAR CRYSTAL CONTACTS
ComponentsFERRITIN
KeywordsMETAL BINDING PROTEIN / IRON STORAGE
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / 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 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsArtymiuk, P.J. / Harrison, P.M.
CitationJournal: Nature / Year: 1991
Title: Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts.
Authors: Lawson, D.M. / Artymiuk, P.J. / Yewdall, S.J. / Smith, J.M. / Livingstone, J.C. / Treffry, A. / Luzzago, A. / Levi, S. / Arosio, P. / Cesareni, G. / Thomas, C.D. / Shaw, W.V. / Harrison, P.M.
History
DepositionDec 20, 1990Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 29, 2012Group: Database references
Revision 1.5Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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_database_status.process_site / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THERE IS A STRAND FROM 84 TO 86 THAT FORMS A TENUOUS TWO-STRANDED ANIT-PARALLEL BETA SHEET ...SHEET THERE IS A STRAND FROM 84 TO 86 THAT FORMS A TENUOUS TWO-STRANDED ANIT-PARALLEL BETA SHEET WITH THE EQUIVALENT STRAND IN A TWO-FOLD RELATED SUBUNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3914
Polymers21,2551
Non-polymers1363
Water36020
1
A: FERRITIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)513,37596
Polymers510,11124
Non-polymers3,26472
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 area90720 Å2
ΔGint-550 kcal/mol
Surface area137520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)184.800, 184.800, 184.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Atom site foot note1: RESIDUE 161 IS A CIS PROLINE.
Components on special symmetry positions
IDModelComponents
11A-210-

CA

21A-211-

CA

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Components

#1: Protein FERRITIN


Mass: 21254.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02794
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FERROXIDASE CENTER WHICH CATALYSES THE OXIDATION OF FE(II) TO FE(III) INVOLVES THE FOLLOWING ...THE FERROXIDASE CENTER WHICH CATALYSES THE OXIDATION OF FE(II) TO FE(III) INVOLVES THE FOLLOWING RESIDUES: GLU 26, GLU 62, HIS 64, FE 200. COORDINATION CONSIDERATIONS SUGGEST THAT THIS FE IS REALLY A CALCIUM ION IN THIS STRUCTURE.
Sequence detailsTHE FERRITIN SEQUENCE CLONED IN ESCHERICHIA COLI WAS THAT OF HOMO SAPIENS EXCEPT THAT LYS 86 WAS ...THE FERRITIN SEQUENCE CLONED IN ESCHERICHIA COLI WAS THAT OF HOMO SAPIENS EXCEPT THAT LYS 86 WAS CHANGED TO GLN FOR THE REASON GIVEN IN REMARK 5. RESIDUE NUMBERING WAS CHOSEN TO BE CONSISTENT WITH THE RAT L CHAIN FERRITIN WHICH HAS AN EIGHT RESIDUE INSERTION (RELATIVE TO HUMAN FERRITIN) FROM 162 - 169 (INCLUSIVE). THESE EIGHT RESIDUES ARE NOT PRESENT IN HUMAN H FERRITIN. THUS IN HUMAN H FERRITIN THE RESIDUE NUMBERING GOES DIRECTLY FROM 161 TO 170 BUT NO RESIDUES ARE MISSING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.23 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 10318 / % possible obs: 95 % / Num. measured all: 54965 / Rmerge(I) obs: 0.128

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.205 / Highest resolution: 2.4 Å
Details: THE STRUCTURE WAS SOLVED BY GENETICALLY ENGINEERING INTERMOLECULAR CRYSTAL CONTACTS FROM THE KNOWN STRUCTURE OF HORSE L CHAIN FERRITIN INTO HUMAN H CHAIN FERRITIN.
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 3 20 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0360.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.025
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.0380.2
X-RAY DIFFRACTIONp_singtor_nbd0.210.5
X-RAY DIFFRACTIONp_multtor_nbd0.1960.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1360.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS

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