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- PDB-4lpm: Frog M-ferritin with magnesium, D127E mutant -

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Basic information

Entry
Database: PDB / ID: 4lpm
TitleFrog M-ferritin with magnesium, D127E mutant
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
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 / Resolution: 1.65 Å
AuthorsTorres, R. / Behera, R. / Goulding, C.W. / Theil, E.C.
CitationJournal: To be Published
Title: D127E ion channel exit modification in ferritin nanocages entraps Fe(II) and impairs its distribution to diiron catalytic centers
Authors: Behera, R. / Torres, R. / Takehiko, T. / Bradley, J. / Goulding, C.W. / Theil, E.C.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / 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_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_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_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)20,89918
Polymers20,4191
Non-polymers48017
Water5,495305
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)501,576432
Polymers490,05424
Non-polymers11,522408
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 area94390 Å2
ΔGint-292 kcal/mol
Surface area138350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.913, 183.913, 183.913
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-202-

MG

31A-203-

CL

41A-209-

MG

51A-210-

MG

61A-213-

MG

71A-214-

CL

81A-305-

HOH

91A-332-

HOH

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Components

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


Mass: 20418.934 Da / Num. of mol.: 1 / Mutation: D127E
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2M MgCl2, 0.1M Bicine, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2012
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 20.8 % / Av σ(I) over netI: 51.77 / Number: 678016 / Rmerge(I) obs: 0.081 / Χ2: 1.33 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 32597 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555010010.0361.59519.8
2.823.5510010.0672.43620.5
2.462.8210010.0972.51321.1
2.242.4610010.1041.87621.1
2.082.2410010.1061.20121
1.962.0810010.1360.94221
1.861.9610010.1860.82220.9
1.781.8610010.2270.66220.9
1.711.7810010.3010.61720.9
1.651.7110010.3760.58620.9
ReflectionResolution: 1.65→50 Å / Num. obs: 32597 / % possible obs: 100 % / Redundancy: 20.8 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.081 / Χ2: 1.333 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.7120.90.37631770.5861100
1.71-1.7820.90.30131950.6171100
1.78-1.8620.90.22732200.6621100
1.86-1.9620.90.18631870.8221100
1.96-2.08210.13632020.9421100
2.08-2.24210.10632221.2011100
2.24-2.4621.10.10432611.8761100
2.46-2.8221.10.09732732.5131100
2.82-3.5520.50.06733112.4361100
3.55-5019.80.03635491.5951100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementResolution: 1.65→45.978 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.919 / SU ML: 0.13 / σ(F): 0 / Phase error: 13.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1637 1968 6.12 %
Rwork0.1258 30177 -
obs0.128 32145 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.99 Å2 / Biso mean: 16.7968 Å2 / Biso min: 2.9 Å2
Refinement stepCycle: LAST / Resolution: 1.65→45.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 17 305 1756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091571
X-RAY DIFFRACTIONf_angle_d1.1792128
X-RAY DIFFRACTIONf_chiral_restr0.061217
X-RAY DIFFRACTIONf_plane_restr0.005288
X-RAY DIFFRACTIONf_dihedral_angle_d13.86607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6503-1.69150.18251360.11342061219796
1.6915-1.73730.17871310.10312067219896
1.7373-1.78840.16181360.10082074221097
1.7884-1.84610.16511370.09732080221798
1.8461-1.91210.16441400.09972122226298
1.9121-1.98870.14351370.10022101223898
1.9887-2.07920.1421370.10212123226099
2.0792-2.18880.14351390.09972144228399
2.1888-2.32590.14731410.101621642305100
2.3259-2.50550.14891400.11521772317100
2.5055-2.75760.18341440.124921872331100
2.7576-3.15650.15571450.133722182363100
3.1565-3.97660.14441470.133822412388100
3.9766-45.99610.20771580.177124182576100

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