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- PDB-3re7: Copper (II) loaded Bullfrog Ferritin M chain -

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Basic information

Entry
Database: PDB / ID: 3re7
TitleCopper (II) loaded Bullfrog Ferritin M chain
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / four-helix bundle / iron storage
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
COPPER (II) ION / Ferritin, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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
DepositionApr 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 / _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

Downloads & links

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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)505,251186
Polymers494,95624
Non-polymers10,294162
Water14,502805
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95350 Å2
ΔGint-316 kcal/mol
Surface area136260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.205, 210.205, 322.803
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 162 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7 mg/mL apo-ferritin solution in TrisHCl at pH 7.5 with 2.5M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.378 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 2.82→48.5 Å / Num. all: 197992 / Num. obs: 197992 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 56.05 Å2 / Rsym value: 0.138 / Net I/σ(I): 7.8
Reflection shellResolution: 2.82→2.97 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 28648 / Rsym value: 0.363 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFR

1mfr


Resolution: 2.82→48.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 9961 -RANDOM
Rwork0.16984 ---
all0.17255 187932 --
obs0.17255 187932 99.96 %-
Displacement parametersBiso mean: 35.955 Å2
Refine analyzeLuzzati coordinate error free: 0.277 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.82→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34032 0 162 805 34999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_angle_deg1.854
X-RAY DIFFRACTIONo_dihedral_angle_d6.013
LS refinement shellResolution: 2.82→2.893 Å
RfactorNum. reflection% reflection
Rfree0.359 729 -
Rwork0.269 --
obs-13728 99.96 %

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