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- PDB-31yr: Horse spleen Apoferritin 0.97 MGy variable temperature dose serie... -

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Basic information

Entry
Database: PDB / ID: 31yr
TitleHorse spleen Apoferritin 0.97 MGy variable temperature dose series, 120 K
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / metal storage / dose series / temperature series
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 / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSouthworth-Davies, R.J. / Garman, E.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Separating the effects of temperature and dose on unit cell volume
Authors: Southworth-Davies, R.J. / Murray, J.W. / Carmichael, I. / Rudino-Pinera, E. / Weik, M. / Garman, E.F.
History
DepositionJun 29, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2104
Polymers19,8721
Non-polymers3373
Water1,54986
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)485,03296
Polymers476,93824
Non-polymers8,09472
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation10_555-y,z,-x1
point symmetry operation11_555y,-z,-x1
point symmetry operation12_555-y,-z,x1
point symmetry operation13_555y,x,-z1
point symmetry operation14_555-y,-x,-z1
point symmetry operation15_555y,-x,z1
point symmetry operation16_555-y,x,z1
point symmetry operation17_555x,z,-y1
point symmetry operation18_555-x,z,y1
point symmetry operation19_555-x,-z,-y1
point symmetry operation2_555-x,-y,z1
point symmetry operation20_555x,-z,y1
point symmetry operation21_555z,y,-x1
point symmetry operation22_555z,-y,x1
point symmetry operation23_555-z,y,x1
point symmetry operation24_555-z,-y,-x1
point symmetry operation3_555-x,y,-z1
point symmetry operation4_555x,-y,-z1
point symmetry operation5_555z,x,y1
point symmetry operation6_555z,-x,-y1
point symmetry operation7_555-z,-x,y1
point symmetry operation8_555-z,x,-y1
point symmetry operation9_555y,z,x1
MethodPISA
Unit cell
Length a, b, c (Å)181.476, 181.476, 181.476
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
11X-201-

CD

21X-202-

CD

31X-203-

CD

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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 genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Equus caballus (horse) / References: UniProt: P02791
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 20 mg/ml protein, 0.6M (NH4)SO4, 10 mM CdSO4 Cryoprotection buffer was the mother liquor with 40% of the water replaced by glycerol

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.15→104.83 Å / Num. obs: 13767 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 22.4 Å2 / Rrim(I) all: 0.08 / Net I/σ(I): 25
Reflection shellResolution: 2.15→2.21 Å / Mean I/σ(I) obs: 5.7 / Num. unique obs: 1052 / Rrim(I) all: 0.33

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→104.83 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.515 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21678 729 5 %RANDOM
Rwork0.19161 ---
obs0.19284 13767 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.229 Å2
Refinement stepCycle: 1 / Resolution: 2.15→104.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 3 86 1487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211428
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9621923
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95524.28677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22615260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.041511
X-RAY DIFFRACTIONr_chiral_restr0.1440.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021091
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2977
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3850.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4690.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3021.5897
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05821370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4453605
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4214.5553
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 62 -
Rwork0.177 990 -
obs--100 %

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