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- PDB-7xz4: Crystal structure of ferritin from Setaria italica -

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Basic information

Entry
Database: PDB / ID: 7xz4
TitleCrystal structure of ferritin from Setaria italica
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin / Setaria italica. Crystal strucutre
Function / homology
Function and homology information


: / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / 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
: / PHOSPHATE ION / Ferritin
Similarity search - Component
Biological speciesSetaria italica (foxtail millet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, W.M. / Wang, Y. / Wang, H.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118 China
National Natural Science Foundation of China (NSFC)21601112 China
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Extension Peptide of Plant Ferritin from Setaria italica Presents a Novel Fold.
Authors: Wang, W. / Wang, Y. / Xi, H. / Song, Z. / Zhang, W. / Xie, L. / Ma, D. / Qin, N. / Wang, H.
History
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,69817
Polymers23,7271
Non-polymers97216
Water2,018112
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)592,763408
Polymers569,44024
Non-polymers23,323384
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 area162110 Å2
ΔGint-849 kcal/mol
Surface area149970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.336, 150.336, 150.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

21A-508-

HOH

31A-511-

HOH

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Components

#1: Protein Ferritin


Mass: 23726.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Setaria italica (foxtail millet) / Gene: 101778084, SETIT_8G019400v2 / Production host: Escherichia coli (E. coli) / References: UniProt: K3ZJM0, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Ammonium dihydrogen phosphate 2.2M,Tris 0.1M, pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27759 / % possible obs: 100 % / Redundancy: 48.4 % / Biso Wilson estimate: 30.29 Å2 / Rmerge(I) obs: 0.567 / Rpim(I) all: 0.081 / Rrim(I) all: 0.573 / Χ2: 1.02 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2419.31.667350.4980.3881.7060.758100
2.24-2.2821.71.7667350.9120.3891.8090.752100
2.28-2.3224.71.7357550.8650.3581.7730.779100
2.32-2.3728.61.7027400.9310.3231.7330.802100
2.37-2.4232.51.6527370.8680.2931.6790.86100
2.42-2.48371.6777470.9590.2771.70.843100
2.48-2.5441.61.527490.9450.2371.5390.879100
2.54-2.6146.61.5327380.9710.2251.5490.868100
2.61-2.6955.61.3777370.9730.1851.3890.922100
2.69-2.7762.21.2437530.9850.1591.2530.941100
2.77-2.8765.11.0397370.9880.131.0470.99100
2.87-2.9965.30.8357640.9860.1050.8421.087100
2.99-3.1265.70.687530.9730.0850.6861.16100
3.12-3.2965.90.5787650.9870.0730.5831.212100
3.29-3.4963.50.4247510.9940.0550.4281.276100
3.49-3.7659.50.347680.9920.0460.3431.341100
3.76-4.14570.2627690.9960.0360.2641.341100
4.14-4.7451.20.1847790.9970.0270.1861.15199.9
4.74-5.9753.10.1617970.9980.0230.1630.998100
5.97-5049.20.0788560.9990.0110.0790.512100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J4J

6j4j


Resolution: 2.2→37.58 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 2756 9.93 %
Rwork0.1581 25003 -
obs0.1624 27759 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.14 Å2 / Biso mean: 36.2657 Å2 / Biso min: 16.72 Å2
Refinement stepCycle: final / Resolution: 2.2→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 24 112 1781
Biso mean--86.1 38.84 -
Num. residues----203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.230.28521290.193111889
2.23-2.270.23011300.1934122494
2.27-2.320.22071350.1799121497
2.32-2.360.21451390.18011265100
2.36-2.420.23181380.17181265100
2.42-2.470.21211390.16641253100
2.47-2.530.19381380.16441258100
2.53-2.60.19321380.15381253100
2.6-2.680.1851360.15261250100
2.68-2.760.23231400.16091276100
2.77-2.860.19121370.1531258100
2.86-2.980.16911390.16591269100
2.98-3.110.18041350.14541262100
3.11-3.280.22441460.16171270100
3.28-3.480.19881380.14781250100
3.48-3.750.17361400.13891273100
3.75-4.130.17041350.13091270100
4.13-4.720.18621430.1343125399
4.73-5.940.23161400.17461263100
5.95-37.580.21451410.1898125998

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