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- PDB-7ryw: Crystal structure of Ferritin grown by the microbatch method in t... -

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Basic information

Entry
Database: PDB / ID: 7ryw
TitleCrystal structure of Ferritin grown by the microbatch method in the presence of Agarose
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / ferritin / crystallization / agarose / metal ions
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / 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: 2.09 Å
AuthorsAditya, S. / Priyadharshine, R. / Maham, I. / Miller, D.J. / Stojanoff, V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Crystal structure of Ferritin grown by microbatch method in the presence of agarose
Authors: Aditya, S. / Priyadharshine, R. / Maham, I. / Miller, D.J. / Stojanoff, V.
History
DepositionAug 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,43015
Polymers19,8721
Non-polymers1,55714
Water1,78399
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)514,316360
Polymers476,93824
Non-polymers37,378336
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 area94570 Å2
ΔGint-539 kcal/mol
Surface area135360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.507, 181.507, 181.507
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-

CD

21A-202-

CD

31A-203-

CD

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Components

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1 / Fragment: residues 3-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: P02791
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 60.76 %
Crystal growTemperature: 290 K / Method: microbatch / Details: CdSO4, NH4SO4, Tris pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→28.7 Å / Num. obs: 15632 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.112 / Net I/σ(I): 0.935
Reflection shellResolution: 2.09→2.15 Å / Num. unique obs: 1090 / CC1/2: 0.954

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W0O

2w0o


Resolution: 2.09→28.7 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 813 5.2 %
Rwork0.17 14816 -
obs0.1713 15629 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.38 Å2 / Biso mean: 30.9457 Å2 / Biso min: 16.77 Å2
Refinement stepCycle: final / Resolution: 2.09→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 17 99 1474
Biso mean--63.33 39.44 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061407
X-RAY DIFFRACTIONf_angle_d0.7731899
X-RAY DIFFRACTIONf_chiral_restr0.039208
X-RAY DIFFRACTIONf_plane_restr0.006249
X-RAY DIFFRACTIONf_dihedral_angle_d4.658190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.09-2.220.2621390.176423802519
2.23-2.40.21991410.179923952536
2.4-2.640.17281200.181424402560
2.64-3.020.20191260.184424512577
3.02-3.80.21151400.166424872627
3.8-28.70.17081470.159126632810

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