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- PDB-2cei: Recombinant human H ferritin, K86Q mutant, soaked with Zn -

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Basic information

Entry
Database: PDB / ID: 2cei
TitleRecombinant human H ferritin, K86Q mutant, soaked with Zn
ComponentsFERRITIN HEAVY CHAIN
KeywordsOXIDOREDUCTASE / APOFERRITIN / FERROXIDASE / DI-IRON / NON-HEME PROTEIN / IRON STORAGE
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / 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 / membrane / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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
DepositionFeb 7, 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 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 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)21,7789
Polymers21,2551
Non-polymers5238
Water2,540141
1
A: FERRITIN HEAVY CHAIN
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)522,669216
Polymers510,11124
Non-polymers12,559192
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)179.419, 179.419, 179.419
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-2136-

HOH

51A-2139-

HOH

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Components

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


Mass: 21254.605 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SOAKED WITH ZN / 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.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 86 TO GLN
Sequence detailsMUTATION K86Q

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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: 7.5
Details: HANGING DROP. RESERVOIR: MPD 21%, CACL2 5.7 MM, HEPES 50 MM PH 7.5 DROP: 2 UL PROTEIN (4.5 MG/ML) AND 1 UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2005 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.8→63.4 Å / Num. obs: 21636 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 29.22 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.3 / % possible all: 95

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Processing

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

2fha


Resolution: 1.8→103.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.076 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1126 5.2 %RANDOM
Rwork0.174 ---
obs0.175 20509 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→103.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 8 141 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211442
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9431943
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0135171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44225.18183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50315262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.221157
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_refined0.2040.2697
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21001
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.111.5889
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74821366
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1823634
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.94.5577
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
Rfree0.333 80
Rwork0.262 1537

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