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

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Basic information

Entry
Database: PDB / ID: 7jgm
TitleCrystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with meta-benzenedihyrdoxamate
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 / 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
NICKEL (II) ION / N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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

Downloads & links

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Assembly

Deposited unit
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
U: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
a: Ferritin heavy chain
b: Ferritin heavy chain
c: Ferritin heavy chain
d: Ferritin heavy chain
e: Ferritin heavy chain
f: Ferritin heavy chain
g: Ferritin heavy chain
h: Ferritin heavy chain
i: Ferritin heavy chain
j: Ferritin heavy chain
k: Ferritin heavy chain
l: Ferritin heavy chain
m: Ferritin heavy chain
n: Ferritin heavy chain
o: Ferritin heavy chain
p: Ferritin heavy chain
q: Ferritin heavy chain
r: Ferritin heavy chain
s: Ferritin heavy chain
t: Ferritin heavy chain
u: Ferritin heavy chain
v: Ferritin heavy chain
w: Ferritin heavy chain
x: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,020,268148
Polymers1,013,87048
Non-polymers6,398100
Water46,1722563
1
A: Ferritin heavy chain
B: Ferritin heavy chain
C: Ferritin heavy chain
D: Ferritin heavy chain
E: Ferritin heavy chain
F: Ferritin heavy chain
G: Ferritin heavy chain
H: Ferritin heavy chain
I: Ferritin heavy chain
J: Ferritin heavy chain
K: Ferritin heavy chain
L: Ferritin heavy chain
M: Ferritin heavy chain
N: Ferritin heavy chain
O: Ferritin heavy chain
P: Ferritin heavy chain
Q: Ferritin heavy chain
R: Ferritin heavy chain
S: Ferritin heavy chain
T: Ferritin heavy chain
U: Ferritin heavy chain
V: Ferritin heavy chain
W: Ferritin heavy chain
X: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)510,13474
Polymers506,93524
Non-polymers3,19950
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
m: Ferritin heavy chain
n: Ferritin heavy chain
o: Ferritin heavy chain
hetero molecules

g: Ferritin heavy chain
h: Ferritin heavy chain
i: Ferritin heavy chain
hetero molecules

j: Ferritin heavy chain
k: Ferritin heavy chain
l: Ferritin heavy chain
hetero molecules

p: Ferritin heavy chain
q: Ferritin heavy chain
r: Ferritin heavy chain
hetero molecules

a: Ferritin heavy chain
b: Ferritin heavy chain
c: Ferritin heavy chain
hetero molecules

d: Ferritin heavy chain
e: Ferritin heavy chain
f: Ferritin heavy chain
hetero molecules

s: Ferritin heavy chain
t: Ferritin heavy chain
u: Ferritin heavy chain
hetero molecules

v: Ferritin heavy chain
w: Ferritin heavy chain
x: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)510,13474
Polymers506,93524
Non-polymers3,19950
Water30617
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-x+1,y+1/2,-z-11
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_755-x+2,y+1/2,-z1
crystal symmetry operation2_754-x+2,y+1/2,-z-11
Unit cell
Length a, b, c (Å)213.550, 213.750, 155.930
Angle α, β, γ (deg.)90.000, 90.048, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 48
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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-V9D / N~1~,N~3~-dihydroxybenzene-1,3-dicarboxamide


Mass: 196.160 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H8N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2563 / 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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL total volume: 40 mM CHES (pH 8.5), 120 mM NaCl, 0.474 mM NiCl2, 10% PEP Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 5 mM m-bdh 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: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 598668 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.69 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.8
Reflection shellResolution: 2.31→2.37 Å / Num. unique obs: 44404 / CC1/2: 0.503

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Processing

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

5cmq


Resolution: 2.31→38.46 Å / SU ML: 0.3254 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 59800 10 %
Rwork0.187 538448 -
obs0.1929 598248 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.12 Å2
Refinement stepCycle: LAST / Resolution: 2.31→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68688 0 204 2563 71455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089105448
X-RAY DIFFRACTIONf_angle_d0.9985142108
X-RAY DIFFRACTIONf_chiral_restr0.048414765
X-RAY DIFFRACTIONf_plane_restr0.005518922
X-RAY DIFFRACTIONf_dihedral_angle_d5.934513650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.340.337520090.279517953X-RAY DIFFRACTION98.51
2.34-2.360.334819940.261818004X-RAY DIFFRACTION98.46
2.36-2.390.342819920.27117918X-RAY DIFFRACTION98.54
2.39-2.420.329519950.261417988X-RAY DIFFRACTION98.43
2.42-2.450.32819680.255217931X-RAY DIFFRACTION98.32
2.45-2.490.32519810.252617902X-RAY DIFFRACTION97.98
2.49-2.520.328419780.246317867X-RAY DIFFRACTION97.93
2.52-2.560.324219380.249717392X-RAY DIFFRACTION95.56
2.56-2.60.339519970.253617969X-RAY DIFFRACTION98.18
2.6-2.640.295420150.223118149X-RAY DIFFRACTION99.11
2.64-2.690.279719910.217517983X-RAY DIFFRACTION98.97
2.69-2.740.283620130.210618091X-RAY DIFFRACTION98.94
2.74-2.790.28919990.217917929X-RAY DIFFRACTION98.73
2.79-2.850.267320210.205618058X-RAY DIFFRACTION98.61
2.85-2.910.27719980.202118006X-RAY DIFFRACTION98.69
2.91-2.980.268819960.192618001X-RAY DIFFRACTION98.57
2.98-3.050.265319960.197117910X-RAY DIFFRACTION98
3.05-3.130.256419530.187917439X-RAY DIFFRACTION95.86
3.13-3.230.259319810.186517982X-RAY DIFFRACTION98.13
3.23-3.330.255920040.187118121X-RAY DIFFRACTION99.06
3.33-3.450.254420060.180418073X-RAY DIFFRACTION98.9
3.45-3.590.226719980.165218049X-RAY DIFFRACTION98.56
3.59-3.750.213920170.149517985X-RAY DIFFRACTION98.44
3.75-3.950.213420010.155818045X-RAY DIFFRACTION98.39
3.95-4.20.190119610.140617608X-RAY DIFFRACTION96.05
4.2-4.520.181320190.129618112X-RAY DIFFRACTION99.41
4.52-4.970.177820190.133218221X-RAY DIFFRACTION99.11
4.97-5.690.204519910.162317973X-RAY DIFFRACTION98.12
5.69-7.160.262119840.213617903X-RAY DIFFRACTION97.07
7.16-38.460.241819850.220617886X-RAY DIFFRACTION96.22

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