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

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Basic information

Entry
Database: PDB / ID: 7jgq
TitleCrystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate collected at 278K after one heating/cooling cycle
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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 3.01 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 21, 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
Water57632
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)156.142, 156.142, 156.142
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-329-

HOH

61A-330-

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 / Feature type: SUBJECT OF INVESTIGATION
#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.: 32 / Source method: isolated from a natural source / Formula: H2O
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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 9.5), 150 mM NaCl, 0.474 mM NiCl2, 12.6% PEP Sitting Drop: 12.7 uL reservoir, 3.3 uL of 25 uM ferritin, 4 uL of 10 mM fdh in 50 mM CHES (pH 9.5) with 150 mM NaCl

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Data collection

DiffractionMean temperature: 278 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Sep 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.01→49.38 Å / Num. obs: 12219 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 10.41 Å2 / CC1/2: 0.973 / Net I/σ(I): 11.4
Reflection shellResolution: 3.01→3.12 Å / Num. unique obs: 1124 / CC1/2: 0.616

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Processing

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

5cmq


Resolution: 3.01→49.38 Å / SU ML: 0.3376 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.8081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2511 1207 9.96 %
Rwork0.195 10916 -
obs0.2005 12123 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.44 Å2
Refinement stepCycle: LAST / Resolution: 3.01→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1425 0 17 32 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221489
X-RAY DIFFRACTIONf_angle_d0.52042011
X-RAY DIFFRACTIONf_chiral_restr0.0358207
X-RAY DIFFRACTIONf_plane_restr0.0025270
X-RAY DIFFRACTIONf_dihedral_angle_d7.0982196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.130.31111340.26191200X-RAY DIFFRACTION100
3.13-3.270.31211370.22721235X-RAY DIFFRACTION100
3.27-3.450.28731370.21121232X-RAY DIFFRACTION100
3.45-3.660.26241330.18771196X-RAY DIFFRACTION100
3.66-3.940.22861340.1781227X-RAY DIFFRACTION100
3.95-4.340.25261320.16821228X-RAY DIFFRACTION100
4.34-4.960.21721320.16321177X-RAY DIFFRACTION97.4
4.97-6.240.22021340.19881194X-RAY DIFFRACTION97.5
6.26-49.380.18511340.1711227X-RAY DIFFRACTION98.98
Refinement TLS params.Method: refined / Origin x: 10.2797321144 Å / Origin y: 39.4388539737 Å / Origin z: 28.969491048 Å
111213212223313233
T0.122235389606 Å2-0.0391651579365 Å2-0.0360774273626 Å2-0.0480261428 Å2-0.125252330613 Å2--0.0878965640134 Å2
L-0.00115306036839 °20.00347877522124 °20.00346679806148 °2-0.00510294004744 °20.00489822183262 °2--0.00353428874367 °2
S0.0222323957466 Å °-0.0203294158052 Å °0.0244791689255 Å °0.0182582018147 Å °0.0054037427874 Å °-0.0136703091385 Å °-0.00790861062357 Å °0.025998426491 Å °0.0292818473024 Å °
Refinement TLS groupSelection details: all

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