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

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Basic information

Entry
Database: PDB / ID: 7jgl
TitleCrystal Structure of the Zn-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 / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / 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 / membrane / 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
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: 2.34 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

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)1,023,838196
Polymers1,013,87048
Non-polymers9,968148
Water31,7781764
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)512,477101
Polymers506,93524
Non-polymers5,54277
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)511,36095
Polymers506,93524
Non-polymers4,42571
Water18010
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)213.990, 213.900, 156.330
Angle α, β, γ (deg.)90.000, 90.136, 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-V9Y / N~2~,N~5~-dihydroxyfuran-2,5-dicarboxamide


Mass: 186.122 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H6N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1764 / 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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 500 uL total volume: 25 mM CHES (pH 8.5), 75 mM NaCl, 0.474 mM ZnCl2, 10% PEP Sitting Drop: 7.6 uL reservoir, 2 uL of 25 uM ferritin, 2.4 uL of 5 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: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 558216 / % possible obs: 94.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.02 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.24
Reflection shellResolution: 2.34→2.4 Å / Num. unique obs: 30818 / CC1/2: 0.761

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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: 2.34→38.49 Å / SU ML: 0.3828 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.43
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2778 55666 9.98 %
Rwork0.2071 502340 -
obs0.2142 558006 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.25 Å2
Refinement stepCycle: LAST / Resolution: 2.34→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68688 0 244 1764 70696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095105400
X-RAY DIFFRACTIONf_angle_d1.0632142040
X-RAY DIFFRACTIONf_chiral_restr0.049614760
X-RAY DIFFRACTIONf_plane_restr0.005718912
X-RAY DIFFRACTIONf_dihedral_angle_d20.431739416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.370.340313200.267112064X-RAY DIFFRACTION67.97
2.37-2.390.355613660.259812746X-RAY DIFFRACTION72.38
2.39-2.420.353915190.258113505X-RAY DIFFRACTION76.85
2.42-2.450.356615950.261314487X-RAY DIFFRACTION81.59
2.45-2.490.338416700.229715245X-RAY DIFFRACTION86.36
2.49-2.520.329517920.239316335X-RAY DIFFRACTION92.23
2.52-2.560.33119370.238317386X-RAY DIFFRACTION99.08
2.56-2.590.33419390.243117580X-RAY DIFFRACTION99.36
2.59-2.640.331919490.240517552X-RAY DIFFRACTION99.41
2.64-2.680.319519470.237817532X-RAY DIFFRACTION99.23
2.68-2.720.323919570.23417427X-RAY DIFFRACTION99.01
2.72-2.770.327819170.240117492X-RAY DIFFRACTION98.99
2.77-2.830.322319260.24317418X-RAY DIFFRACTION98.56
2.83-2.890.30119300.228217278X-RAY DIFFRACTION97.71
2.89-2.950.31618710.221716824X-RAY DIFFRACTION95.39
2.95-3.020.298219150.223417405X-RAY DIFFRACTION98.22
3.02-3.090.301719340.216817453X-RAY DIFFRACTION99.23
3.09-3.180.29119460.216317498X-RAY DIFFRACTION98.96
3.18-3.270.285319430.221117543X-RAY DIFFRACTION98.95
3.27-3.370.294919360.217817411X-RAY DIFFRACTION98.78
3.37-3.490.287619250.215917341X-RAY DIFFRACTION98.12
3.49-3.630.2718790.196816954X-RAY DIFFRACTION95.59
3.63-3.80.25619520.188617386X-RAY DIFFRACTION98.45
3.8-40.252319670.189817562X-RAY DIFFRACTION99.37
4-4.250.24319570.176317528X-RAY DIFFRACTION99.16
4.25-4.580.240619460.177617532X-RAY DIFFRACTION98.62
4.58-5.040.225719030.16717230X-RAY DIFFRACTION97.11
5.04-5.760.235919340.177317679X-RAY DIFFRACTION99.34
5.77-7.260.268719340.201217348X-RAY DIFFRACTION97.65
7.26-38.490.242919600.205917599X-RAY DIFFRACTION97.82

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