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- PDB-3se1: Frog M-ferritin with magnesium, R72D mutant -

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Basic information

Entry
Database: PDB / ID: 3se1
TitleFrog M-ferritin with magnesium, R72D mutant
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / IRON STORAGE / DIIRON / METAL-BINDING
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: 1.65 Å
AuthorsTosha, T. / Ng, H.L. / Alber, T. / Theil, E.C.
CitationJournal: TO BE PUBLISHED
Title: Frog M-ferritin with magnesium, R72D mutant
Authors: Tosha, T. / Ng, H.L. / Alber, T. / Theil, E.C.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,11919
Polymers20,5811
Non-polymers53818
Water4,432246
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)506,854456
Polymers493,94624
Non-polymers12,908432
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_577x,-y+2,-z+21
crystal symmetry operation5_465z-1,x+1,y1
crystal symmetry operation6_467z-1,-x+1,-y+21
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_667-z+1,x+1,-y+21
crystal symmetry operation9_456y-1,z,x+11
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_476y-1,-z+2,-x+11
crystal symmetry operation12_676-y+1,-z+2,x+11
crystal symmetry operation13_467y-1,x+1,-z+21
crystal symmetry operation14_667-y+1,-x+1,-z+21
crystal symmetry operation15_465y-1,-x+1,z1
crystal symmetry operation16_665-y+1,x+1,z1
crystal symmetry operation17_557x,z,-y+21
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_577-x,-z+2,-y+21
crystal symmetry operation20_575x,-z+2,y1
crystal symmetry operation21_456z-1,y,-x+11
crystal symmetry operation22_476z-1,-y+2,x+11
crystal symmetry operation23_656-z+1,y,x+11
crystal symmetry operation24_676-z+1,-y+2,-x+11
Buried area80800 Å2
ΔGint-289 kcal/mol
Surface area140590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.560, 183.560, 183.560
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-184-

MG

21A-186-

CL

31A-386-

HOH

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Components

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


Mass: 20581.074 Da / Num. of mol.: 1 / Mutation: R72D
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-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.0 M MgCl2, 100 mM BICINE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.65→106 Å / Num. all: 32417 / Num. obs: 32417 / % possible obs: 100 % / Redundancy: 20.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 22.6
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.1187 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→91.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.189 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20329 1643 5.1 %RANDOM
Rwork0.17213 ---
obs0.17368 30760 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.955 Å2
Refinement stepCycle: LAST / Resolution: 1.65→91.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 18 246 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0211463
X-RAY DIFFRACTIONr_bond_other_d0.0020.021023
X-RAY DIFFRACTIONr_angle_refined_deg2.4431.9521981
X-RAY DIFFRACTIONr_angle_other_deg1.55932500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0085186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32124.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8215282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8361510
X-RAY DIFFRACTIONr_chiral_restr0.1890.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021657
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02304
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_it1.4381.5858
X-RAY DIFFRACTIONr_mcbond_other0.4511.5346
X-RAY DIFFRACTIONr_mcangle_it2.53421384
X-RAY DIFFRACTIONr_scbond_it4.3153605
X-RAY DIFFRACTIONr_scangle_it6.9684.5586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 101 -
Rwork0.35 2242 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 27.3414 Å / Origin y: 174.547 Å / Origin z: 143.0494 Å
111213212223313233
T0.0826 Å2-0.0129 Å20.0121 Å2-0.0654 Å2-0.0074 Å2--0.0649 Å2
L1.5411 °2-0.4483 °20.7634 °2-0.8424 °2-0.4894 °2--0.6637 °2
S0.0218 Å °-0.0333 Å °-0.0763 Å °0.0276 Å °-0.0039 Å °0.0213 Å °0.0419 Å °0.0053 Å °-0.0178 Å °

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