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- PDB-4lpn: Frog M-ferritin with cobalt, D127E mutant -

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Basic information

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


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / 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: 1.66 Å
AuthorsTorres, R. / Behera, R. / Goulding, C.W.
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: Torres, R. / Behera, 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 1.2Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_struct_special_symmetry ...pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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)21,67724
Polymers20,6371
Non-polymers1,04023
Water3,477193
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)520,259576
Polymers495,29324
Non-polymers24,966552
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area97330 Å2
ΔGint-516 kcal/mol
Surface area134650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.003, 184.003, 184.003
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-205-

CO

21A-206-

CO

31A-207-

CO

41A-209-

CO

51A-212-

CL

61A-219-

CL

71A-221-

MG

81A-317-

HOH

91A-337-

HOH

101A-390-

HOH

111A-482-

HOH

Detailsbiological unit is the same as asym.

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Components

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


Mass: 20637.207 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 193 / 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 / Method: vapor diffusion, hanging drop / pH: 9
Details: 2M MgCl2, 0.1M Bicine, 0.1M CoCl2, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: 18.6 % / Av σ(I) over netI: 31.65 / Number: 596172 / Rmerge(I) obs: 0.079 / Χ2: 0.95 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 32085 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555099.910.0470.84919.3
2.823.5510010.0691.01820.7
2.462.8210010.0731.00221
2.242.4610010.0910.75720.6
2.082.2410010.1061.04519.9
1.962.0810010.1610.84419
1.861.9610010.2440.92918.3
1.781.8610010.2781.08617.4
1.711.7810010.3871.05115.1
1.651.718310.4860.96813.3
ReflectionResolution: 1.65→50 Å / Num. obs: 32085 / % possible obs: 98.3 % / Redundancy: 18.6 % / Biso Wilson estimate: 16.56 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.95 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.7113.30.48626480.968183
1.71-1.7815.10.38731911.0511100
1.78-1.8617.40.27832071.0861100
1.86-1.9618.30.24431850.9291100
1.96-2.08190.16132180.8441100
2.08-2.2419.90.10632371.0451100
2.24-2.4620.60.09132510.7571100
2.46-2.82210.07332831.0021100
2.82-3.5520.70.06933191.0181100
3.55-5019.30.04735460.849199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KA4

3ka4


Resolution: 1.66→46.001 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9028 / SU ML: 0.15 / σ(F): 0 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1768 1972 6.27 %RANDOM
Rwork0.1586 ---
obs0.1597 31474 98.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.21 Å2 / Biso mean: 19.8055 Å2 / Biso min: 9.29 Å2
Refinement stepCycle: LAST / Resolution: 1.66→46.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 23 193 1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021614
X-RAY DIFFRACTIONf_angle_d1.1692105
X-RAY DIFFRACTIONf_chiral_restr0.065215
X-RAY DIFFRACTIONf_plane_restr0.006285
X-RAY DIFFRACTIONf_dihedral_angle_d14.175595
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 (%)
1.6596-1.70110.18331330.171986211995
1.7011-1.74710.20651350.16682019215496
1.7471-1.79860.22621370.16192042217996
1.7986-1.85660.20481370.15022051218898
1.8566-1.9230.19841380.17352011214995
1.923-20.19281380.15322049218797
2-2.0910.19231370.15422063220097
2.091-2.20120.16391410.136521142255100
2.2012-2.33910.16931390.14462096223598
2.3391-2.51970.15751430.138621432286100
2.5197-2.77330.17661450.152221662311100
2.7733-3.17450.15571440.154921802324100
3.1745-3.99920.16261470.152822052352100
3.9992-46.01840.18791580.188123772535100

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