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- PDB-7jgk: Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-... -

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Basic information

Entry
Database: PDB / ID: 7jgk
TitleCrystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate collected at 100K
ComponentsFerritin heavy chain
KeywordsOXIDOREDUCTASE / Protein-MOF / Ferritin-MOF / Self-Assembly / Ferritin
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 / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / 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
NICKEL (II) ION / N~2~,N~5~-dihydroxyfuran-2,5-dicarboxamide / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsBailey, J.B. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0003844 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Tunable and Cooperative Thermomechanical Properties of Protein-Metal-Organic Frameworks.
Authors: Bailey, J.B. / Tezcan, F.A.
History
DepositionJul 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 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)21,5076
Polymers21,1221
Non-polymers3855
Water46826
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)516,180144
Polymers506,93524
Non-polymers9,245120
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)155.990, 155.990, 155.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Space group name HallI423
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+1/2,y+1/2,z+1/2
#26: x+1/2,-z+1/2,y+1/2
#27: x+1/2,z+1/2,-y+1/2
#28: z+1/2,y+1/2,-x+1/2
#29: -z+1/2,y+1/2,x+1/2
#30: -y+1/2,x+1/2,z+1/2
#31: y+1/2,-x+1/2,z+1/2
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1/2,x+1/2
#35: z+1/2,-x+1/2,-y+1/2
#36: -y+1/2,z+1/2,-x+1/2
#37: -z+1/2,-x+1/2,y+1/2
#38: -z+1/2,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1/2
#40: x+1/2,-y+1/2,-z+1/2
#41: -x+1/2,y+1/2,-z+1/2
#42: -x+1/2,-y+1/2,z+1/2
#43: y+1/2,x+1/2,-z+1/2
#44: -y+1/2,-x+1/2,-z+1/2
#45: z+1/2,-y+1/2,x+1/2
#46: -z+1/2,-y+1/2,-x+1/2
#47: -x+1/2,z+1/2,y+1/2
#48: -x+1/2,-z+1/2,-y+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

V9Y

21A-202-

NI

31A-203-

NI

41A-205-

NA

51A-317-

HOH

61A-321-

HOH

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Components

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


Mass: 21122.291 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-V9Y / N~2~,N~5~-dihydroxyfuran-2,5-dicarboxamide


Mass: 186.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O5
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.74 Å3/Da / Density % sol: 67.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL total volume: 31 mM CHES (pH 10), 93 mM NaCl, 0.474 mM NiCl2, 12% PEP Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 10 mM H2fdh in 50 mM CHES (pH 9.5) with 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.68→36.77 Å / Num. obs: 9313 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 58.17 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.1
Reflection shellResolution: 2.68→2.81 Å / Num. unique obs: 1223 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CMQ

5cmq


Resolution: 2.68→36.77 Å / SU ML: 0.2624 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2859
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 458 4.94 %
Rwork0.197 8804 -
obs0.1993 9262 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.63 Å2
Refinement stepCycle: LAST / Resolution: 2.68→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 17 26 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01241481
X-RAY DIFFRACTIONf_angle_d1.20821998
X-RAY DIFFRACTIONf_chiral_restr0.0557206
X-RAY DIFFRACTIONf_plane_restr0.0066268
X-RAY DIFFRACTIONf_dihedral_angle_d7.1328193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.780.3828480.2821864X-RAY DIFFRACTION98.7
2.78-2.890.3293430.2525870X-RAY DIFFRACTION99.35
2.89-3.020.2915390.2329864X-RAY DIFFRACTION98.05
3.02-3.180.2888360.2588865X-RAY DIFFRACTION97.93
3.18-3.380.3256460.2447879X-RAY DIFFRACTION98.93
3.38-3.640.2475580.1933846X-RAY DIFFRACTION97.94
3.64-40.2465430.1843877X-RAY DIFFRACTION98.19
4-4.580.1967370.1631900X-RAY DIFFRACTION98.84
4.58-5.760.2123520.1674883X-RAY DIFFRACTION96.99
5.77-36.770.2213560.1897956X-RAY DIFFRACTION97.31
Refinement TLS params.Method: refined / Origin x: 10.2153636485 Å / Origin y: 39.3840110475 Å / Origin z: 28.748828799 Å
111213212223313233
T0.828604466453 Å2-0.0937854348113 Å2-0.0822710351618 Å2-0.494990304685 Å2-0.273847263159 Å2--0.632616694196 Å2
L1.30194457265 °2-0.276794952702 °20.689040234415 °2-0.583850053736 °2-0.574195257651 °2--1.90561695085 °2
S-0.0180930054873 Å °-0.365149738642 Å °0.495527356584 Å °0.461778442964 Å °0.0457980375354 Å °-0.219989556178 Å °-0.568781098667 Å °0.144796827915 Å °-0.0202036074918 Å °
Refinement TLS groupSelection details: all

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