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- PDB-8xwb: Crystal structure of dinitrosyl iron units binding with human hea... -

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Basic information

Entry
Database: PDB / ID: 8xwb
TitleCrystal structure of dinitrosyl iron units binding with human heavy chain Ferritin
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / Human 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
: / NITRIC OXIDE / Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsGong, W.J. / Wang, W.M. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118 China
CitationJournal: Spectrochim Acta A Mol Biomol Spectrosc / Year: 2024
Title: Insight into the photodynamic mechanism and protein binding of a nitrosyl iron-sulfur [Fe 2 S 2 (NO) 4 ] 2- cluster.
Authors: Gong, W. / Wu, T. / Liu, Y. / Jiao, S. / Wang, W. / Yan, W. / Li, Y. / Liu, Y. / Zhang, Y. / Wang, H.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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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)20,57913
Polymers20,1171
Non-polymers46312
Water4,774265
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)493,901312
Polymers482,79724
Non-polymers11,104288
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
Buried area103700 Å2
ΔGint-532 kcal/mol
Surface area142820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.680, 183.680, 183.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-205-

MG

21A-206-

MG

31A-209-

CL

41A-210-

CL

51A-319-

HOH

61A-552-

HOH

71A-558-

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: 20116.547 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

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Non-polymers , 5 types, 277 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Bicine,Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 30026 / % possible obs: 99.9 % / Redundancy: 35 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.014 / Rrim(I) all: 0.08 / Χ2: 2.359 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.73290.35714600.9860.9960.0670.3631.021100
1.73-1.7630.80.33314680.9890.9970.0610.3381.071100
1.76-1.79330.29214800.9920.9980.0510.2971.222100
1.79-1.8336.80.25714690.9940.9990.0430.261.302100
1.83-1.8737.40.23714660.9960.9990.0390.241.389100
1.87-1.9137.20.2114850.9950.9990.0350.2131.578100
1.91-1.9636.40.18714520.9960.9990.0320.191.777100
1.96-2.0234.80.16914940.9980.9990.0290.1721.942100
2.02-2.0736.90.14714750.9970.9990.0250.152.128100
2.07-2.14370.13114780.9980.9990.0220.1322.348100
2.14-2.2236.60.11214830.99910.0190.1142.469100
2.22-2.3135.20.10414830.99910.0180.1052.589100
2.31-2.4137.20.09315100.99910.0150.0942.744100
2.41-2.5438.20.08314900.99910.0140.0842.666100
2.54-2.737.40.07515070.99910.0120.0762.686100
2.7-2.9136.60.06615080.99910.0110.0672.864100
2.91-3.237.90.0611534110.010.0623.173100
3.2-3.6634.90.05915340.99910.010.063.524100
3.66-4.6133.40.06315740.99910.0110.0644.203100
4.61-5026.20.06416760.99910.0130.0654.18198.2

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FTV

6ftv


Resolution: 1.69→42.14 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 2000 6.66 %
Rwork0.1588 --
obs0.1612 30026 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 14 265 1676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081448
X-RAY DIFFRACTIONf_angle_d1.0431953
X-RAY DIFFRACTIONf_dihedral_angle_d4.731190
X-RAY DIFFRACTIONf_chiral_restr0.056205
X-RAY DIFFRACTIONf_plane_restr0.007258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.20971400.1621963X-RAY DIFFRACTION100
1.74-1.780.19241390.15691948X-RAY DIFFRACTION100
1.78-1.840.18551400.14941966X-RAY DIFFRACTION100
1.84-1.90.19691400.1631957X-RAY DIFFRACTION100
1.9-1.960.15341410.14981976X-RAY DIFFRACTION100
1.96-2.040.17071400.1521960X-RAY DIFFRACTION100
2.04-2.130.16381410.14761984X-RAY DIFFRACTION100
2.13-2.250.17021420.14351984X-RAY DIFFRACTION100
2.25-2.390.18481410.15891979X-RAY DIFFRACTION100
2.39-2.570.20031430.16632007X-RAY DIFFRACTION100
2.57-2.830.22631440.17112013X-RAY DIFFRACTION100
2.83-3.240.19471450.15862022X-RAY DIFFRACTION100
3.24-4.080.20141480.14622070X-RAY DIFFRACTION100
4.08-42.140.20661560.1742197X-RAY DIFFRACTION99

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