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- PDB-8j11: Crystal structure of horse spleen L-ferritin at 0deg Celsius. -

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Basic information

Entry
Database: PDB / ID: 8j11
TitleCrystal structure of horse spleen L-ferritin at 0deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / 0deg Celsius
Function / homology
Function and homology information


ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / 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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMaity, B. / Tian, J. / Abe, S. / Ueno, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cryst.Growth Des. / Year: 2023
Title: Atomic-Level Insights into a Unique Semi-Clathrate Hydrate Formed in a Confined Environment of Porous Protein Crystal.
Authors: Maity, B. / Tian, J. / Furuta, T. / Abe, S. / Ueno, T.
History
DepositionApr 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6129
Polymers19,8721
Non-polymers7398
Water2,558142
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)494,681216
Polymers476,93824
Non-polymers17,743192
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area95180 Å2
ΔGint-550 kcal/mol
Surface area139120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.084, 182.084, 182.084
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
11X-204-

CD

21X-205-

CD

31X-206-

CD

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Components

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Protein , 1 types, 1 molecules X

#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: Escherichia coli (E. coli) / References: UniProt: P02791

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Non-polymers , 5 types, 150 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM)

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Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→22.091 Å / Num. obs: 34317 / % possible obs: 99.3 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.901 / Num. unique obs: 1619 / CC1/2: 0.46 / Rpim(I) all: 0.622 / Rrim(I) all: 1.102 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
CrysalisProv42data collection
CrysalisProv42data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
Coot0.9.8.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.091 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.542 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1864 1738 5.065 %
Rwork0.155 32573 -
all0.157 --
obs-34311 99.045 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.614 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 19 142 1546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121501
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161428
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.6472038
X-RAY DIFFRACTIONr_angle_other_deg0.5821.5773289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9485196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.155514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73110278
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.2341082
X-RAY DIFFRACTIONr_chiral_restr0.0890.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
X-RAY DIFFRACTIONr_nbd_refined0.2430.2299
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21137
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2721
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1960.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3080.214
X-RAY DIFFRACTIONr_nbd_other0.140.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.233
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2110.28
X-RAY DIFFRACTIONr_mcbond_it1.7291.308715
X-RAY DIFFRACTIONr_mcbond_other1.7081.307715
X-RAY DIFFRACTIONr_mcangle_it2.6372.331898
X-RAY DIFFRACTIONr_mcangle_other2.6372.338899
X-RAY DIFFRACTIONr_scbond_it3.9471.807786
X-RAY DIFFRACTIONr_scbond_other3.8431.781779
X-RAY DIFFRACTIONr_scangle_it6.1113.0761128
X-RAY DIFFRACTIONr_scangle_other6.1013.0231117
X-RAY DIFFRACTIONr_lrange_it7.52715.7571733
X-RAY DIFFRACTIONr_lrange_other7.32814.7211701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6420.3161200.28722950.28925010.9270.9396.56140.277
1.642-1.6860.2571030.25922690.25924340.9470.95197.45280.244
1.686-1.7350.2461250.24222070.24223730.9540.95798.27220.223
1.735-1.7880.2621270.22721550.22823090.9560.96398.83070.206
1.788-1.8460.2251150.20520880.20622190.9640.97199.2790.175
1.846-1.910.211060.18420430.18521620.9710.97799.39870.154
1.91-1.9820.1841000.17819900.17821050.9760.97999.28740.148
1.982-2.0620.164940.15519160.15620210.9840.98599.45570.125
2.062-2.1530.189930.13718280.1419370.9810.98899.1740.112
2.153-2.2570.1491110.1317550.13118660.9860.9891000.108
2.257-2.3780.161870.1217030.12217900.9840.9911000.101
2.378-2.520.147870.11915910.1216810.9870.99199.82150.097
2.52-2.6920.17720.12515210.12716020.9830.99199.43820.1
2.692-2.9040.184700.12614210.12914910.9810.991000.104
2.904-3.1750.191670.13413250.13713920.9790.9891000.112
3.175-3.5410.163770.13411970.13612740.9850.9891000.116
3.541-4.0720.163760.12110620.12411390.9840.99199.91220.109
4.072-4.9450.138480.1179390.1189870.9890.9921000.108
4.945-6.8240.233440.1757570.1788010.9740.9831000.156
6.824-22.0910.251160.1895110.1915310.9660.97699.24670.184

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