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- PDB-8ykr: Enhancing the Gastric Stability of Ferritin Nanocage via Computat... -

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Basic information

Entry
Database: PDB / ID: 8ykr
TitleEnhancing the Gastric Stability of Ferritin Nanocage via Computational-Assisted Disulfide Bond Engineering
ComponentsFerritin
KeywordsBIOSYNTHETIC PROTEIN / Ferritin / Disulfide Bond / Computational-Assisted
Function / homology
Function and homology information


ferroxidase / : / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm
Similarity search - Function
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
Biological speciesPenaeus japonicus (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGu, C.K. / Wang, S.J. / Zhao, G.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030084 China
CitationJournal: To Be Published
Title: Enhancing the Gastric Stability of Ferritin Nanocage via Computational-Assisted Disulfide Bond Engineering
Authors: Gu, C.K. / Wang, S.J. / Zhao, G.H.
History
DepositionMar 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,22816
Polymers116,6706
Non-polymers55810
Water1,06359
1
B: Ferritin
A: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
A: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
A: Ferritin
F: Ferritin
hetero molecules

B: Ferritin
A: Ferritin
F: Ferritin
hetero molecules

C: Ferritin
D: Ferritin
E: Ferritin
hetero molecules

C: Ferritin
D: Ferritin
E: Ferritin
hetero molecules

C: Ferritin
D: Ferritin
E: Ferritin
hetero molecules

C: Ferritin
D: Ferritin
E: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,91464
Polymers466,68024
Non-polymers2,23440
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_455x-1/2,y+1/2,z+1/21
crystal symmetry operation6_545-x+1/2,-y-1/2,z+1/21
crystal symmetry operation7_445-y-1/2,x-1/2,z+1/21
crystal symmetry operation8_555y+1/2,-x+1/2,z+1/21
Buried area91000 Å2
ΔGint-1108 kcal/mol
Surface area135190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.080, 125.080, 175.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Ferritin


Mass: 19445.004 Da / Num. of mol.: 6
Mutation: A44C, K72C, H125C, L135C, V139C, D147C, A155C, Y163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus japonicus (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2B7E1, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: sodium phosphate monobasic monohydrate, potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 46591 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.043 / Rrim(I) all: 0.112 / Χ2: 0.596 / Net I/σ(I): 4.7 / Num. measured all: 314666
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.80.80123270.7460.9240.3320.8680.44100
2.54-2.596.70.68622930.7860.9380.2870.7440.449100
2.59-2.646.50.59523530.8210.9490.2540.6470.44100
2.64-2.696.90.49222790.8910.9710.2020.5320.457100
2.69-2.7570.46423430.8980.9730.1890.5020.473100
2.75-2.826.90.39623220.9260.9810.1620.4280.485100
2.82-2.896.80.33223290.9390.9840.1370.3590.509100
2.89-2.966.70.30323370.9460.9860.1270.3290.515100
2.96-3.056.30.25323330.9590.990.1090.2760.55100
3.05-3.156.90.20523130.9740.9930.0850.2220.575100
3.15-3.266.50.17123020.9820.9960.0730.1860.596100
3.26-3.396.90.14223360.9860.9960.0580.1530.642100
3.39-3.556.90.1123490.9910.9980.0450.1190.695100
3.55-3.736.90.09623090.9930.9980.040.1040.783100
3.73-3.976.50.0823070.9950.9990.0340.0860.819100
3.97-4.276.80.06723620.9970.9990.0280.0720.833100
4.27-4.76.90.05823320.9970.9990.0240.0630.85100
4.7-5.386.90.05323360.9980.9990.0220.0580.746100
5.38-6.766.50.05423450.9970.9990.0230.0590.588100
6.76-306.60.03123840.99910.0130.0330.44899.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.482 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 2000 4.29 %
Rwork0.1854 --
obs0.1873 46566 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8010 0 10 59 8079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018174
X-RAY DIFFRACTIONf_angle_d1.13910999
X-RAY DIFFRACTIONf_dihedral_angle_d8.577039
X-RAY DIFFRACTIONf_chiral_restr0.051161
X-RAY DIFFRACTIONf_plane_restr0.0061458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56210.33391440.24873151X-RAY DIFFRACTION100
2.5621-2.63140.30611340.22733175X-RAY DIFFRACTION100
2.6314-2.70870.26471560.21223187X-RAY DIFFRACTION100
2.7087-2.79610.28761390.22313152X-RAY DIFFRACTION100
2.7961-2.8960.29661370.22593204X-RAY DIFFRACTION100
2.896-3.01180.29071460.23153138X-RAY DIFFRACTION100
3.0118-3.14870.27491540.22573191X-RAY DIFFRACTION100
3.1487-3.31450.30511320.22263185X-RAY DIFFRACTION100
3.3145-3.52190.23421420.20253174X-RAY DIFFRACTION100
3.5219-3.79330.21841400.17933220X-RAY DIFFRACTION100
3.7933-4.17410.22271390.16323199X-RAY DIFFRACTION100
4.1741-4.77580.16751510.1433167X-RAY DIFFRACTION100
4.7758-6.00870.21881450.17483209X-RAY DIFFRACTION100
6.0087-29.4820.1711410.15113214X-RAY DIFFRACTION99

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