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- PDB-3u90: apoferritin: complex with SDS -

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Basic information

Entry
Database: PDB / ID: 3u90
Titleapoferritin: complex with SDS
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / four helix bundle / iron-binding protein / intracellular protein
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / 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 light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, R. / Bu, W. / Xi, J. / Mortazavi, S.R. / Cheung-Lau, J.C. / Dmochowski, I.J. / Loll, P.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Beyond the detergent effect: a binding site for sodium dodecyl sulfate (SDS) in mammalian apoferritin.
Authors: Liu, R. / Bu, W. / Xi, J. / Mortazavi, S.R. / Cheung-Lau, J.C. / Dmochowski, I.J. / Loll, P.J.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / software
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value ..._pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _software.classification / _software.name / _software.version
Revision 1.3Sep 13, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_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 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,26312
Polymers19,8721
Non-polymers1,39111
Water3,063170
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)510,310288
Polymers476,93824
Non-polymers33,372264
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 area106280 Å2
ΔGint-141 kcal/mol
Surface area132930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.830, 181.830, 181.830
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-176-

CD

21A-308-

HOH

31A-352-

HOH

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Components

#1: Protein Ferritin light chain / / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: spleen / References: UniProt: P02791
#2: Chemical ChemComp-SDS / DODECYL SULFATE / Sodium dodecyl sulfate


Mass: 266.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O4S / Comment: detergent*YM
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M cadmium sulfate, 0.1 M HEPES, 1.0 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 10, 2011
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→19.84 Å / Num. obs: 21314 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 6 / Redundancy: 34.09 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 43.4
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 34.09 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 9 / % possible all: 87.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
CNSrefinement
ADSCQuantumdata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XZ1
Resolution: 1.9→19.84 Å / SU ML: 0.2 / σ(F): 1.54 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 2020 9.51 %RANDOM
Rwork0.1848 ---
obs0.187 21314 98.71 %-
all-39149 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.126 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 27 170 1551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071392
X-RAY DIFFRACTIONf_angle_d0.8971870
X-RAY DIFFRACTIONf_dihedral_angle_d14.547529
X-RAY DIFFRACTIONf_chiral_restr0.065204
X-RAY DIFFRACTIONf_plane_restr0.003243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.90210.179840.25941231X-RAY DIFFRACTION82
1.9021-1.92710.22051310.22871232X-RAY DIFFRACTION95
1.9271-1.95350.29661280.22241309X-RAY DIFFRACTION96
1.9535-1.98130.28551460.20421256X-RAY DIFFRACTION97
1.9813-2.01090.21611500.17671310X-RAY DIFFRACTION99
2.0109-2.04230.19461730.1821297X-RAY DIFFRACTION99
2.0423-2.07570.19571480.1641298X-RAY DIFFRACTION100
2.0757-2.11150.16551440.17041328X-RAY DIFFRACTION100
2.1115-2.14980.2291490.17551309X-RAY DIFFRACTION100
2.1498-2.19110.19541290.18031328X-RAY DIFFRACTION100
2.1911-2.23580.22911230.18051318X-RAY DIFFRACTION100
2.2358-2.28430.22891360.1811361X-RAY DIFFRACTION100
2.2843-2.33740.22681430.19261323X-RAY DIFFRACTION100
2.3374-2.39580.18461410.17611328X-RAY DIFFRACTION100
2.3958-2.46040.19111390.17451286X-RAY DIFFRACTION100
2.4604-2.53270.21491520.18011346X-RAY DIFFRACTION100
2.5327-2.61420.22161440.18031302X-RAY DIFFRACTION100
2.6142-2.70750.21881720.16491300X-RAY DIFFRACTION100
2.7075-2.81560.19271400.17931341X-RAY DIFFRACTION100
2.8156-2.94330.20931660.17931282X-RAY DIFFRACTION100
2.9433-3.0980.18311500.17511316X-RAY DIFFRACTION100
3.098-3.29120.22031330.17921337X-RAY DIFFRACTION100
3.2912-3.5440.21131070.1761373X-RAY DIFFRACTION100
3.544-3.89820.19931390.15611336X-RAY DIFFRACTION100
3.8982-4.45670.19691650.16511299X-RAY DIFFRACTION100
4.4567-5.59410.15951380.18891334X-RAY DIFFRACTION100
5.5941-19.84020.20281340.21311345X-RAY DIFFRACTION100

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