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- PDB-6wyf: Crystal structure of Human H-chain Ferritin variant 157C Delta C-... -

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Basic information

Entry
Database: PDB / ID: 6wyf
TitleCrystal structure of Human H-chain Ferritin variant 157C Delta C-star Modified with a RAFT Agent Soaked in an Acrylate Solution
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Ferritin / Polymer / Hydrogel / Polymer Integrated Crystals / Crystal Hydrogel Hybrids / RAFT Polymerization
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / 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
: / Chem-RFT / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBailey, J.B. / Zhang, L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2020
Title: Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks.
Authors: Han, K. / Bailey, J.B. / Zhang, L. / Tezcan, F.A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,01116
Polymers21,0591
Non-polymers95215
Water5,927329
1
A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules

A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,271384
Polymers505,42124
Non-polymers22,850360
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
Unit cell
Length a, b, c (Å)179.940, 179.940, 179.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Space group name HallF423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x,y+1/2,z+1/2
#26: x,-z+1/2,y+1/2
#27: x,z+1/2,-y+1/2
#28: z,y+1/2,-x+1/2
#29: -z,y+1/2,x+1/2
#30: -y,x+1/2,z+1/2
#31: y,-x+1/2,z+1/2
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y,x+1/2,-z+1/2
#44: -y,-x+1/2,-z+1/2
#45: z,-y+1/2,x+1/2
#46: -z,-y+1/2,-x+1/2
#47: -x,z+1/2,y+1/2
#48: -x,-z+1/2,-y+1/2
#49: x+1/2,y,z+1/2
#50: x+1/2,-z,y+1/2
#51: x+1/2,z,-y+1/2
#52: z+1/2,y,-x+1/2
#53: -z+1/2,y,x+1/2
#54: -y+1/2,x,z+1/2
#55: y+1/2,-x,z+1/2
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+1/2,x,-z+1/2
#68: -y+1/2,-x,-z+1/2
#69: z+1/2,-y,x+1/2
#70: -z+1/2,-y,-x+1/2
#71: -x+1/2,z,y+1/2
#72: -x+1/2,-z,-y+1/2
#73: x+1/2,y+1/2,z
#74: x+1/2,-z+1/2,y
#75: x+1/2,z+1/2,-y
#76: z+1/2,y+1/2,-x
#77: -z+1/2,y+1/2,x
#78: -y+1/2,x+1/2,z
#79: y+1/2,-x+1/2,z
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+1/2,x+1/2,-z
#92: -y+1/2,-x+1/2,-z
#93: z+1/2,-y+1/2,x
#94: -z+1/2,-y+1/2,-x
#95: -x+1/2,z+1/2,y
#96: -x+1/2,-z+1/2,-y
Components on special symmetry positions
IDModelComponents
11A-202-

CA

21A-203-

CA

31A-205-

CA

41A-206-

CA

51A-208-

CA

61A-210-

CA

71A-327-

HOH

81A-532-

HOH

91A-579-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 21059.211 Da / Num. of mol.: 1 / Mutation: K86Q, C90E, C102A, C130A, K157C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase

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Non-polymers , 5 types, 344 molecules

#2: Chemical ChemComp-RFT / butyl 1-{[2-(2,5-dioxopyrrolidin-1-yl)ethyl]amino}-2-methyl-1-oxopropan-2-yl carbonotrithioate


Mass: 376.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O3S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 5 uL reservoir + 5 uL 25 uM 157C delta C-star Human H-chain Ferritin in 15 mM HEPES, pH 7.0 against reservoir of 500 uL 25 mM HEPES, pH 8.0, 10 mM calcium chloride, 140 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.25→54.25 Å / Num. obs: 64146 / % possible obs: 93 % / Redundancy: 59.1 % / Biso Wilson estimate: 11.02 Å2 / CC1/2: 1 / Net I/σ(I): 29.5
Reflection shellResolution: 1.25→1.27 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3357 / CC1/2: 0.791

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B8F

6b8f


Resolution: 1.25→36.73 Å / SU ML: 0.0887 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 10.5178
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1307 3246 5.07 %
Rwork0.1132 60823 -
obs0.1142 64069 92.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.53 Å2
Refinement stepCycle: LAST / Resolution: 1.25→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 26 329 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091551
X-RAY DIFFRACTIONf_angle_d1.06462117
X-RAY DIFFRACTIONf_chiral_restr0.0805223
X-RAY DIFFRACTIONf_plane_restr0.0077285
X-RAY DIFFRACTIONf_dihedral_angle_d13.7085227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.22031260.18312815X-RAY DIFFRACTION99.76
1.27-1.290.15711450.15292803X-RAY DIFFRACTION100
1.29-1.310.15871570.13472794X-RAY DIFFRACTION100
1.31-1.330.14421500.122790X-RAY DIFFRACTION100
1.33-1.360.15411520.11382797X-RAY DIFFRACTION100
1.36-1.380.14711470.11932806X-RAY DIFFRACTION99.86
1.38-1.410.25611500.1992769X-RAY DIFFRACTION98.65
1.41-1.440.11281370.0982819X-RAY DIFFRACTION100
1.44-1.470.1116980.08892039X-RAY DIFFRACTION73.89
1.48-1.510.1171200.07642178X-RAY DIFFRACTION100
1.51-1.550.09931140.07952162X-RAY DIFFRACTION76.53
1.55-1.60.10621480.07782817X-RAY DIFFRACTION100
1.6-1.650.11391560.07662832X-RAY DIFFRACTION100
1.65-1.710.11421440.08052823X-RAY DIFFRACTION100
1.71-1.780.11621470.08452843X-RAY DIFFRACTION100
1.78-1.860.11791600.09072815X-RAY DIFFRACTION100
1.86-1.950.10691090.09291636X-RAY DIFFRACTION62.37
1.96-2.070.10861420.09352439X-RAY DIFFRACTION99.92
2.09-2.240.11121400.09112722X-RAY DIFFRACTION99.9
2.24-2.460.12121420.10232526X-RAY DIFFRACTION87.65
2.47-2.820.13641520.11782753X-RAY DIFFRACTION94.35
2.82-3.550.12211600.1222848X-RAY DIFFRACTION96.5
3.56-36.730.15661500.1522997X-RAY DIFFRACTION94.85

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