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- PDB-3rbc: Bullfrog M ferritin with iron(III) bound to the ferroxidase site -

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Basic information

Entry
Database: PDB / ID: 3rbc
TitleBullfrog M ferritin with iron(III) bound to the ferroxidase site
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / four-helix bundle / ferroxidase / iron storage
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / 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 speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBertini, I. / Lalli, D. / Mangani, S. / Pozzi, C. / Rosa, C. / Turano, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structural insights into the ferroxidase site of ferritins from higher eukaryotes.
Authors: Bertini, I. / Lalli, D. / Mangani, S. / Pozzi, C. / Rosa, C. / Theil, E.C. / Turano, P.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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

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Assembly

Deposited unit
A: Ferritin, middle subunit
B: Ferritin, middle subunit
C: Ferritin, middle subunit
D: Ferritin, middle subunit
E: Ferritin, middle subunit
F: Ferritin, middle subunit
G: Ferritin, middle subunit
H: Ferritin, middle subunit
I: Ferritin, middle subunit
J: Ferritin, middle subunit
K: Ferritin, middle subunit
L: Ferritin, middle subunit
M: Ferritin, middle subunit
N: Ferritin, middle subunit
O: Ferritin, middle subunit
P: Ferritin, middle subunit
Q: Ferritin, middle subunit
R: Ferritin, middle subunit
S: Ferritin, middle subunit
T: Ferritin, middle subunit
U: Ferritin, middle subunit
V: Ferritin, middle subunit
W: Ferritin, middle subunit
X: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)497,74974
Polymers494,95624
Non-polymers2,79250
Water27,8331545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95140 Å2
ΔGint-646 kcal/mol
Surface area139430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.719, 210.719, 324.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 20623.182 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli (E. coli) / References: UniProt: P07798, ferroxidase
#2: Chemical...
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1545 / 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: 4.2 Å3/Da / Density % sol: 70.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3M sodium formate, 8% v/v ethylene glycol,20 mM TRIS.HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.2915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2915 Å / Relative weight: 1
ReflectionResolution: 2.7→64.88 Å / Num. obs: 210135 / % possible obs: 92.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 46.042 Å2 / Rsym value: 0.131 / Net I/σ(I): 5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.3 / Num. unique all: 29358 / % possible all: 89.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MFR

1mfr


Resolution: 2.7→61.13 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.928 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23465 10510 5 %RANDOM
Rwork0.17292 ---
all0.176 199524 --
obs0.176 199524 92.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.279 Å-
Luzzati sigma a-0.182 Å
Refinement stepCycle: LAST / Resolution: 2.7→61.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33945 0 50 1545 35540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02134617
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.94746591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08554124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01824.8921950
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.8156323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.20415198
X-RAY DIFFRACTIONr_chiral_restr0.130.24916
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0226654
X-RAY DIFFRACTIONr_mcbond_it0.7611.520620
X-RAY DIFFRACTIONr_mcangle_it1.629232977
X-RAY DIFFRACTIONr_scbond_it2.952313997
X-RAY DIFFRACTIONr_scangle_it5.0984.513614
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 754 -
Rwork0.258 14026 -
obs--88.83 %

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