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- PDB-6i9p: Iron-free state of Rana catesbeiana H' ferritin variant H54N -

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Basic information

Entry
Database: PDB / ID: 6i9p
TitleIron-free state of Rana catesbeiana H' ferritin variant H54N
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / Rana Catesbeiana H' ferritin / ferroxidase process / H54N variant / iron-free state
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / 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, middle subunit
Similarity search - Component
Biological speciesLithobates catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPozzi, C. / Di Pisa, F. / Mangani, S.
CitationJournal: J.Inorg.Biochem. / Year: 2019
Title: Effect of the point mutation H54N on the ferroxidase process of Rana catesbeiana H' ferritin.
Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Turano, P. / Mangani, S.
History
DepositionNov 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,28124
Polymers20,5991
Non-polymers68223
Water6,738374
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)510,739576
Polymers494,37924
Non-polymers16,359552
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 area92710 Å2
ΔGint-323 kcal/mol
Surface area136610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.910, 183.910, 183.910
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-59-

ARG

21A-206-

MG

31A-207-

MG

41A-210-

MG

51A-220-

CL

61A-221-

CL

71A-670-

HOH

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Components

#1: Protein Ferritin, middle subunit / Ferritin M / Ferritin H' / Ferritin X


Mass: 20599.137 Da / Num. of mol.: 1 / Mutation: H54N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lithobates catesbeiana (American bullfrog)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P07798, ferroxidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 8-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.25→21.24 Å / Num. obs: 73567 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.079 / Net I/σ(I): 19.1
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 10565 / Rpim(I) all: 0.122 / Rrim(I) all: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LQH

4lqh


Resolution: 1.25→21.1 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.729 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13327 3705 5 %RANDOM
Rwork0.11688 ---
obs0.11771 69785 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.724 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.116 Å
Refinement stepCycle: 1 / Resolution: 1.25→21.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 23 374 1820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131664
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171502
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.6442276
X-RAY DIFFRACTIONr_angle_other_deg1.6321.5893542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8985225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3823.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60515326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9941511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021945
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02356
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.936775
X-RAY DIFFRACTIONr_mcbond_other0.935774
X-RAY DIFFRACTIONr_mcangle_it1.065984
X-RAY DIFFRACTIONr_mcangle_other1.065985
X-RAY DIFFRACTIONr_scbond_it1.214889
X-RAY DIFFRACTIONr_scbond_other1.214889
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6081270
X-RAY DIFFRACTIONr_long_range_B_refined3.462137
X-RAY DIFFRACTIONr_long_range_B_other2.2962035
X-RAY DIFFRACTIONr_rigid_bond_restr1.4631209
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 280 -
Rwork0.153 5020 -
obs--99.96 %

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