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- PDB-8j10: Crystal structure of horse spleen L-ferritin at -180deg Celsius c... -

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Basic information

Entry
Database: PDB / ID: 8j10
TitleCrystal structure of horse spleen L-ferritin at -180deg Celsius cooled from -20deg Celsius.
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / -180deg Celsius
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 / 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)20,87813
Polymers19,8721
Non-polymers1,00512
Water4,504250
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)501,063312
Polymers476,93824
Non-polymers24,125288
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_554-y,-x,-z-11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_554y,z+1/2,x-1/21
crystal symmetry operation34_554-y,z+1/2,-x-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation41_554x,z+1/2,-y-1/21
crystal symmetry operation42_554-x,z+1/2,y-1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_544x,-z-1/2,y-1/21
crystal symmetry operation53_554z+1/2,x,y-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation55_454-z-1/2,-x,y-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation69_554z+1/2,y,-x-1/21
crystal symmetry operation70_554z+1/2,-y,x-1/21
crystal symmetry operation71_454-z-1/2,y,x-1/21
crystal symmetry operation72_454-z-1/2,-y,-x-1/21
Buried area92080 Å2
ΔGint-300 kcal/mol
Surface area141840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.786, 180.786, 180.786
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-201-

CD

21X-202-

CD

31X-526-

HOH

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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 / Plasmid: PMK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02791

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
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: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.6→22.096 Å / Num. obs: 33540 / % possible obs: 99.1 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.056 / Rrim(I) all: 0.126 / Net I/σ(I): 8.8
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1686 / CC1/2: 0.53 / Rpim(I) all: 0.649 / Rrim(I) all: 1.162

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Processing

Software
NameVersionClassification
CrysalisProv42data collection
CrysalisProv42data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
REFMAC5.8.0403refinement
Coot0.9.8.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.096 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.736 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2058 1649 4.923 %
Rwork0.1797 31845 -
all0.181 --
obs-33494 98.799 %
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: 12.117 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 40 250 1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121512
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161431
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6532044
X-RAY DIFFRACTIONr_angle_other_deg0.5661.5793289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9685192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.959515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13210275
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.9321084
X-RAY DIFFRACTIONr_chiral_restr0.0810.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined0.2490.2344
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21232
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2716
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.2806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2171
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2440.21
X-RAY DIFFRACTIONr_metal_ion_refined0.290.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.370.233
X-RAY DIFFRACTIONr_nbd_other0.2260.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2060.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.090.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3340.28
X-RAY DIFFRACTIONr_mcbond_it1.5611.098711
X-RAY DIFFRACTIONr_mcbond_other1.5611.097711
X-RAY DIFFRACTIONr_mcangle_it2.4561.956892
X-RAY DIFFRACTIONr_mcangle_other2.4561.961893
X-RAY DIFFRACTIONr_scbond_it2.5861.421801
X-RAY DIFFRACTIONr_scbond_other2.5851.426802
X-RAY DIFFRACTIONr_scangle_it4.12.4421142
X-RAY DIFFRACTIONr_scangle_other4.0982.4471143
X-RAY DIFFRACTIONr_lrange_it6.24315.9941893
X-RAY DIFFRACTIONr_lrange_other6.24316.011894
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
1.6-1.6420.2731110.27322980.27324390.9420.94498.770.262
1.642-1.6860.241170.2622080.25923560.9620.95198.68420.245
1.686-1.7350.2511200.2521850.2523330.9580.95698.79980.232
1.735-1.7880.241050.23721170.23722510.9630.96198.71170.216
1.788-1.8460.207970.21220620.21121880.9720.96998.67460.187
1.846-1.9110.2471250.20819600.2121360.9640.97197.61240.18
1.911-1.9820.1991000.19218990.19320350.9730.97698.2310.165
1.982-2.0620.2021000.17418350.17519920.9770.98197.13860.145
2.062-2.1530.1781010.15217720.15419020.9780.98698.47530.129
2.153-2.2570.186950.15917160.1618190.980.98599.56020.132
2.257-2.3780.177950.14616390.14817360.980.98699.88480.121
2.378-2.520.177790.14515770.14716570.9810.98799.93970.121
2.52-2.6920.201740.14114900.14415660.9710.98899.87230.12
2.692-2.9040.164630.15214080.15314710.9840.9861000.128
2.904-3.1760.205600.15312980.15513580.9780.9851000.133
3.176-3.5410.193580.16311780.16512410.980.98599.59710.147
3.541-4.0720.199410.15510650.15611170.9760.98699.01520.143
4.072-4.9450.159440.1519200.1529680.9840.98599.58680.14
4.945-6.8250.307370.2447360.2467840.9540.97298.59690.217
6.825-22.0960.251270.2184820.2195260.9690.97196.76810.214

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