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- PDB-4ml5: one minute iron loaded frog M ferritin mutant H54Q -

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Basic information

Entry
Database: PDB / ID: 4ml5
Titleone minute iron loaded frog M ferritin mutant H54Q
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / one minute 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: 1.22 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 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 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_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)21,62330
Polymers20,6131
Non-polymers1,00929
Water6,882382
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)518,941720
Polymers494,71624
Non-polymers24,225696
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_455-x-1,z,y1
crystal symmetry operation19_455-x-1,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation58_454-y-1/2,z,-x-1/21
crystal symmetry operation59_454y-1/2,-z,-x-1/21
crystal symmetry operation60_455-y-1/2,-z,x+1/21
crystal symmetry operation69_454z-1/2,y,-x-1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_455-z-1/2,y,x+1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation78_445z-1/2,-x-1/2,-y1
crystal symmetry operation79_445-z-1/2,-x-1/2,y1
crystal symmetry operation80_455-z-1/2,x+1/2,-y1
crystal symmetry operation85_455y-1/2,x+1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_445y-1/2,-x-1/2,z1
crystal symmetry operation88_455-y-1/2,x+1/2,z1
Buried area108140 Å2
ΔGint-1591 kcal/mol
Surface area136750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.230, 184.230, 184.230
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-

MG

21A-207-

MG

31A-209-

MG

41A-220-

CL

51A-221-

CL

61A-413-

HOH

71A-670-

HOH

81A-680-

HOH

91A-681-

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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6-2M magnesium chloride, 0.1M bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.954
SYNCHROTRONELETTRA 5.2R21.751, 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
21.7511
31.7391
ReflectionResolution: 1.22→22.51 Å / Num. all: 1071136 / Num. obs: 79449 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Biso Wilson estimate: 8.162 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.22-1.298.60.3755.1113911,2100
3.86-22.5113.30.03538.3371691,299.5

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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: 1.22→21.71 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.731 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15352 3987 5 %RANDOM
Rwork0.13904 ---
obs0.13976 75437 99.96 %-
all-75437 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.357 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.22→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 29 382 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191567
X-RAY DIFFRACTIONr_bond_other_d0.0010.021479
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.9522132
X-RAY DIFFRACTIONr_angle_other_deg0.84133440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5465205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16925.27591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49215308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.699159
X-RAY DIFFRACTIONr_chiral_restr0.0580.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_rigid_bond_restr4.20231567
X-RAY DIFFRACTIONr_sphericity_free14.237570
X-RAY DIFFRACTIONr_sphericity_bonded4.59451862
LS refinement shellResolution: 1.22→1.252 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 305 -
Rwork0.169 5450 -
obs-75437 100 %

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