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- PDB-2iu2: Recombinant human H ferritin, K86Q, E27D and E107D mutant, soaked... -

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Basic information

Entry
Database: PDB / ID: 2iu2
TitleRecombinant human H ferritin, K86Q, E27D and E107D mutant, soaked with Zn ions
ComponentsFERRITIN HEAVY CHAIN
KeywordsOXIDOREDUCTASE / IRON / APOFERRITIN / FERROXIDASE / IRON STORAGE / METAL-BINDING / PHOSPHORYLATION / DI-IRON NON-HEME PROTEIN
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 / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsToussaint, L. / Crichton, R.R. / Declercq, J.P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: High-Resolution X-Ray Structures of Human Apoferritin H-Chain Mutants Correlated with Their Activity and Metal-Binding Sites.
Authors: Toussaint, L. / Bertrand, L. / Hue, L. / Crichton, R.R. / Declercq, J.P.
History
DepositionMay 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRITIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7118
Polymers21,2271
Non-polymers4857
Water2,738152
1
A: FERRITIN HEAVY CHAIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)521,066192
Polymers509,43724
Non-polymers11,629168
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation24_555-z,-y,-x1
MethodPQS
Unit cell
Length a, b, c (Å)181.050, 181.050, 181.050
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-210-

ZN

21A-211-

ZN

31A-214-

ZN

41A-2036-

HOH

51A-2150-

HOH

61A-2152-

HOH

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Components

#1: Protein FERRITIN HEAVY CHAIN / PROLIFERATION-INDUCING GENE 15 PROTEIN / FERRITIN H SUBUNIT / RECOMBINANT HUMAN H APOFERRITIN


Mass: 21226.553 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M5219 / References: UniProt: P02794, ferroxidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 27 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 86 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 27 TO ASP ENGINEERED RESIDUE IN CHAIN A, LYS 86 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLU 107 TO ASP
Sequence detailsMUTATION K86Q,E27D,E107D

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP. RESERVOIR : MPD 5.2%, CACL2 3.9 MM, TRIS 50 MM PH 8.5. DROP: 1UL PROTEIN (24 MG/ML) AND 1 UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979661
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2005
Details: TWO CRYSTALS MONOCHROMATOR BETWEEN TWO CYLINDRICAL PARABOLIC MIRRORS
RadiationMonochromator: FIRST CRYSTALSFLAT AND N2 COOLED. SECOND CRYSTAL SAGITALLY BENT
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979661 Å / Relative weight: 1
ReflectionResolution: 1.8→45.26 Å / Num. obs: 24095 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 18.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHI

2chi


Resolution: 1.8→104.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.104 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1230 5.1 %RANDOM
Rwork0.193 ---
obs0.195 22887 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→104.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 12 152 1575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211445
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9451946
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1395171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27725.18183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91415260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.777157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021115
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2667
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21007
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0281.5887
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6521366
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9823638
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6154.5580
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 82
Rwork0.235 1667

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