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- PDB-4mn9: Fifteen minutes iron loaded frog M ferritin mutant H54Q -

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Basic information

Entry
Database: PDB / ID: 4mn9
TitleFifteen minutes iron loaded frog M ferritin mutant H54Q
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / fifteen minutes iron soaking / four helix bundle / ferroxidase
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 speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Sep 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_ref_seq_dif / 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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,49725
Polymers20,6131
Non-polymers88424
Water6,359353
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)515,933600
Polymers494,71624
Non-polymers21,217576
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area92340 Å2
ΔGint-313 kcal/mol
Surface area137510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.930, 183.930, 183.930
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-206-

FE

21A-207-

MG

31A-208-

MG

41A-210-

MG

51A-224-

CL

61A-345-

HOH

71A-374-

HOH

81A-412-

HOH

91A-441-

HOH

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Components

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


Mass: 20613.162 Da / Num. of mol.: 1 / Mutation: H54Q
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


Mass: 55.845 Da / Num. of mol.: 6 / 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.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 60.88 %
Crystal growTemperature: 277 K / 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF BM1410.954
SYNCHROTRONELETTRA 5.2R21.761, 1.739
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDOct 8, 2012MIRROR
DECTRIS PILATUS 2M2PIXELOct 29, 2012MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI111SINGLE WAVELENGTHMx-ray1
2SI111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9541
21.7611
31.7391
ReflectionResolution: 1.15→22.47 Å / Num. obs: 93348 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.7
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.3 / % possible all: 95

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KA3

3ka3


Resolution: 1.15→22.47 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.642 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 4670 5 %RANDOM
Rwork0.141 ---
obs0.141 88648 99.1 %-
all-93318 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.93 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.15→22.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 24 353 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191568
X-RAY DIFFRACTIONr_bond_other_d0.0010.021477
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.9512136
X-RAY DIFFRACTIONr_angle_other_deg1.93933431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3115206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42425.16193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85315306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.891510
X-RAY DIFFRACTIONr_chiral_restr0.0540.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02380
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.8431340
X-RAY DIFFRACTIONr_sphericity_free17.142572
X-RAY DIFFRACTIONr_sphericity_bonded5.75551612
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 305 -
Rwork0.223 5968 -
obs--92.13 %

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