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- PDB-4my7: frog M ferritin iron-loaded under anaerobic environment -

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Basic information

Entry
Database: PDB / ID: 4my7
Titlefrog M ferritin iron-loaded under anaerobic environment
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / four helix bundle / ferroxidase / cytoplasm anaerobic
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / 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, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMangani, S. / Di Pisa, F. / Pozzi, C. / Turano, P. / Lalli, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Time-lapse anomalous X-ray diffraction shows how Fe(2+) substrate ions move through ferritin protein nanocages to oxidoreductase sites.
Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Theil, E. / Turano, P. / Mangani, S.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Non-polymer description
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,31020
Polymers20,6231
Non-polymers68619
Water6,215345
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)511,430480
Polymers494,95624
Non-polymers16,473456
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 area106470 Å2
ΔGint-1636 kcal/mol
Surface area132770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.830, 183.830, 183.830
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-205-

FE2

21A-206-

MG

31A-207-

MG

41A-211-

MG

51A-212-

MG

61A-217-

CL

71A-358-

HOH

81A-395-

HOH

91A-443-

HOH

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Components

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


Mass: 20623.182 Da / Num. of mol.: 1
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6-2M magnesium chloride, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976, 1.722, 1.758
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013 / Details: mirror
RadiationMonochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
21.7221
31.7581
ReflectionResolution: 1.48→49.96 Å / Num. all: 433231 / Num. obs: 55514 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.48-1.569.20.424.7584361100
4.68-45.968.70.06329.714149199.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KA3

3ka3


Resolution: 1.48→41.11 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.904 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19504 2255 5 %RANDOM
Rwork0.17446 ---
all0.17548 44719 --
obs0.17548 42464 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.48→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 19 345 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191484
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9472009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3915187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27124.69983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41515280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.333159
X-RAY DIFFRACTIONr_chiral_restr0.0740.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021149
X-RAY DIFFRACTIONr_sphericity_free11.315511
X-RAY DIFFRACTIONr_sphericity_bonded35.39557
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 171 -
Rwork0.224 3042 -
obs-42464 99.91 %

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