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- PDB-1mfr: CRYSTAL STRUCTURE OF M FERRITIN -

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Basic information

Entry
Database: PDB / ID: 1mfr
TitleCRYSTAL STRUCTURE OF M FERRITIN
ComponentsM FERRITIN
KeywordsIRON STORAGE / DIIRON
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: 2.8 Å
AuthorsHa, Y. / Shi, D. / Allewell, N.M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1999
Title: Crystal structure of bullfrog M ferritin at 2.8 A resolution: analysis of subunit interactions and the binuclear metal center
Authors: Ha, Y. / Shi, D. / Small, W. / Theil, E.C. / Allewell, N.M.
History
DepositionJun 18, 1998Processing site: BNL
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M FERRITIN
B: M FERRITIN
C: M FERRITIN
D: M FERRITIN
E: M FERRITIN
F: M FERRITIN
G: M FERRITIN
H: M FERRITIN
I: M FERRITIN
J: M FERRITIN
K: M FERRITIN
L: M FERRITIN
M: M FERRITIN
N: M FERRITIN
O: M FERRITIN
P: M FERRITIN
Q: M FERRITIN
R: M FERRITIN
S: M FERRITIN
T: M FERRITIN
U: M FERRITIN
V: M FERRITIN
W: M FERRITIN
X: M FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,12372
Polymers494,95624
Non-polymers1,16748
Water23,7801320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area93220 Å2
ΔGint-579 kcal/mol
Surface area126100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.800, 210.800, 328.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.351792, -0.854538, -0.38211), (0.14777, 0.352388, -0.924114), (0.924341, -0.38156, 0.002307)61.6025, 208.02049, 237.7778
2given(-0.353156, 0.146268, 0.92406), (-0.853753, 0.353542, -0.382248), (-0.382605, -0.923912, 2.2E-5)-228.5768, 70.0933, 215.35339
3given(0.038685, -0.956361, -0.289615), (0.994944, 0.009982, 0.099937), (-0.092684, -0.292017, 0.951912)85.4528, 160.8028, 33.3215
4given(-0.923193, 0.040483, -0.3822), (0.038856, -0.979511, -0.197607), (-0.382369, -0.19728, 0.902704)-75.128, 251.1022, 11.0147
5given(0.038678, 0.995105, -0.090943), (-0.955615, 0.010234, -0.294441), (-0.292069, 0.098294, 0.951333)-160.37801, 90.0731, -22.9895
6given(-0.423229, -0.257664, 0.868612), (-0.257986, -0.884749, -0.388154), (0.868516, -0.388367, 0.307977)-180.27049, 247.6604, 193.26691
7given(-0.02187, 0.948421, 0.316259), (-0.340106, -0.304526, 0.889715), (0.940133, -0.088103, 0.329223)-214.4675, 3.0912, 161.3127
8given(0.045133, 0.348046, -0.936391), (0.060809, 0.93465, 0.35033), (0.997128, -0.072753, 0.021019)27.6218, -36.9297, 205.16161
9given(0.915429, -0.064308, 0.39731), (-0.394314, 0.054552, 0.917355), (-0.080667, -0.996438, 0.024581)-52.3674, -43.9996, 239.2984
10given(0.439276, 0.233535, -0.867467), (0.897405, -0.158407, 0.411791), (-0.041246, -0.959358, -0.27916)56.4364, 130.9259, 279.21149
11given(-0.828629, 0.438899, -0.347479), (0.443362, 0.13558, -0.886029), (-0.341766, -0.888249, -0.306937)-118.5222, 245.9774, 255.92979
12given(-0.453043, -0.891309, 0.017889), (-0.891283, 0.452416, -0.030558), (0.019144, -0.029788, -0.999373)4.8578, 8.6357, 277.06641
13given(0.044773, 0.068142, 0.99667), (0.353133, 0.932181, -0.079596), (-0.934501, 0.355521, 0.017674)-204.369, 41.0439, 34.3614
14given(0.914526, -0.396763, -0.078872), (-0.061096, 0.057268, -0.996488), (0.399886, 0.916133, 0.028132)49.798, 237.55659, 55.2639
15given(-0.905975, 0.418964, 0.060652), (0.418702, 0.865694, 0.274341), (0.062433, 0.273942, -0.959718)-176.7795, 4.2596, 240.3842
16given(0.376862, 0.85109, 0.365541), (0.850805, -0.474085, 0.22666), (0.366205, 0.225585, -0.902776)-184.7805, 188.65559, 257.47989
17given(0.828946, -0.458803, 0.319919), (-0.458945, -0.884871, -0.079835), (0.319716, -0.080646, -0.944075)-3.0602, 192.83279, 294.3205
18given(0.439432, 0.897294, -0.04199), (0.234448, -0.159691, -0.958923), (-0.867141, 0.411537, -0.280542)-130.41499, 275.6235, 73.0819
19given(0.328411, -0.162074, -0.930526), (-0.160922, -0.980366, 0.113961), (-0.930726, 0.112316, -0.348044)102.228, 196.1227, 111.7777
20given(-0.060876, -0.991977, 0.110795), (-0.041666, 0.11343, 0.992672), (-0.997275, 0.055813, -0.048237)28.6307, -38.611, 73.0336
21given(-0.063078, -0.038307, -0.997273), (-0.991805, 0.113647, 0.058367), (0.111101, 0.992782, -0.045162)72.4048, 28.1483, 38.4935
22given(-0.999624, 0.016645, 0.021771), (0.016871, -0.252259, 0.967513), (0.021596, 0.967517, 0.251883)-132.3634, 9.4648, -5.1163
23given(-0.02199, -0.334163, 0.942259), (0.950178, -0.300104, -0.084254), (0.31093, 0.893461, 0.324114)-156.011, 217.8904, 11.6025

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Components

#1: Protein ...
M FERRITIN


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
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1320 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
21.0 MNa/K tartrate1drop
320 mM1dropMgCl2
40.1 Macetate1drop
51.0 MNa/K tartrate1reservoir
60.5 Mammonium sulfate1reservoir
720 mM1reservoirMgCl2
80.1 Macetate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD / Date: Feb 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→10 Å / Num. obs: 141403 / % possible obs: 70 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.064 / Rsym value: 0.076 / Net I/σ(I): 11.1
Reflection shellResolution: 2.8→2.92 Å / % possible all: 27
Reflection
*PLUS
Num. measured all: 249976
Reflection shell
*PLUS
% possible obs: 27 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1RCD

1rcd


Resolution: 2.8→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.194 --
Rwork0.19 --
obs0.19 141403 70 %
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32976 0 48 1320 34344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.375
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg20.444
X-RAY DIFFRACTIONx_improper_angle_deg1.297

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