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- PDB-5j8w: One minute iron loaded Rana Catesbeiana H' ferritin variant E57A/... -

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Basic information

Entry
Database: PDB / ID: 5j8w
TitleOne minute iron loaded Rana Catesbeiana H' ferritin variant E57A/E136A/D140A
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / Rana Catesbeiana / ferritin variant / ferroxidase activity / M type / H' type / oxidoreductase activity / iron
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
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: 1.11 Å
AuthorsPozzi, C. / Di Pisa, F. / Mangani, S. / Bernacchioni, C. / Turano, P.
CitationJournal: Chemistry / Year: 2016
Title: Ferroxidase Activity in Eukaryotic Ferritin is Controlled by Accessory-Iron-Binding Sites in the Catalytic Cavity.
Authors: Bernacchioni, C. / Pozzi, C. / Di Pisa, F. / Mangani, S. / Turano, P.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 10, 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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)21,44731
Polymers20,4631
Non-polymers98430
Water6,702372
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)514,722744
Polymers491,11424
Non-polymers23,608720
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation59_555y+1/2,-z,-x+1/21
crystal symmetry operation60_554-y+1/2,-z,x-1/21
crystal symmetry operation69_555z+1/2,y,-x+1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_554-z+1/2,y,x-1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
crystal symmetry operation77_545z+1/2,x-1/2,y1
crystal symmetry operation78_555z+1/2,-x+1/2,-y1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation80_545-z+1/2,x-1/2,-y1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_555-y+1/2,-x+1/2,-z1
crystal symmetry operation87_555y+1/2,-x+1/2,z1
crystal symmetry operation88_545-y+1/2,x-1/2,z1
Buried area92940 Å2
ΔGint-684 kcal/mol
Surface area139150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.340, 184.340, 184.340
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-202-

CL

21A-209-

CL

31A-223-

MG

41A-225-

MG

51A-226-

MG

61A-230-

MG

71A-511-

HOH

81A-596-

HOH

91A-659-

HOH

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Components

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


Mass: 20463.100 Da / Num. of mol.: 1 / Mutation: E57A, E136A, D140A
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-FE2 / FE (II) ION


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


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.3 Å3/Da / Density % sol: 63.5 % / Description: Octahedral crystals
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0039, 1.7220, 1.7587
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 25, 2013
RadiationMonochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00391
21.7221
31.75871
ReflectionResolution: 1.11→18.81 Å / Num. obs: 106549 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.8
Reflection shellResolution: 1.11→1.16 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8S

5j8s


Resolution: 1.11→18.53 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / Rfactor Rfree error: 0.022 / SU B: 0.509 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14101 5310 5 %RANDOM
Rwork0.13064 ---
obs0.13117 101125 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.609 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.11→18.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 30 372 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191594
X-RAY DIFFRACTIONr_bond_other_d0.0020.021499
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9472180
X-RAY DIFFRACTIONr_angle_other_deg2.11633486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6055218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84425.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16415303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.058158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021878
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02384
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_it0.758754
X-RAY DIFFRACTIONr_mcbond_other0.88753
X-RAY DIFFRACTIONr_mcangle_it0.856954
X-RAY DIFFRACTIONr_mcangle_other0.908955
X-RAY DIFFRACTIONr_scbond_it0.927840
X-RAY DIFFRACTIONr_scbond_other0.927840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1321205
X-RAY DIFFRACTIONr_long_range_B_refined2.7442336
X-RAY DIFFRACTIONr_long_range_B_other1.4092000
X-RAY DIFFRACTIONr_rigid_bond_restr7.51731232
X-RAY DIFFRACTIONr_sphericity_free22.235584
X-RAY DIFFRACTIONr_sphericity_bonded8.68451559
LS refinement shellResolution: 1.105→1.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 407 -
Rwork0.161 7333 -
obs--99.97 %

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