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- PDB-7vvs: PLL9 induced TmFtn nanocage -

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Basic information

Entry
Database: PDB / ID: 7vvs
TitlePLL9 induced TmFtn nanocage
ComponentsFerritin
KeywordsPROTEIN BINDING / Thermotoga maritima ferritin / PLL9 / nanocage
Function / homology
Function and homology information


bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhao, G. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972018 China
CitationJournal: To Be Published
Title: PLL9 induced TmFtn nanocage
Authors: Zhao, G. / Zhang, X.
History
DepositionNov 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: 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
H: Ferritin
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,10824
Polymers155,2158
Non-polymers89416
Water14,502805
1
H: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
hetero molecules

H: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
hetero molecules

H: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
hetero molecules

F: Ferritin
hetero molecules

F: Ferritin
hetero molecules

F: Ferritin
hetero molecules

B: Ferritin
hetero molecules

B: Ferritin
hetero molecules

B: Ferritin
hetero molecules

E: Ferritin
G: Ferritin
hetero molecules

E: Ferritin
G: Ferritin
hetero molecules

E: Ferritin
G: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,32572
Polymers465,64424
Non-polymers2,68148
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation4_545y,x-1,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_655-x+1,-x+y,-z1
crystal symmetry operation4_655y+1,x,-z1
crystal symmetry operation5_545x-y,-y-1,-z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation13_544x+1/3,y-1/3,z-1/31
crystal symmetry operation14_544-y+1/3,x-y-1/3,z-1/31
crystal symmetry operation15_544-x+y+1/3,-x-1/3,z-1/31
Buried area70310 Å2
ΔGint-533 kcal/mol
Surface area154010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.193, 176.193, 357.508
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-417-

HOH

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Components

#1: Protein
Ferritin


Mass: 19401.840 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 2 mM PLL9, 100 mM Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97919 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.2→38.685 Å / Num. obs: 107941 / % possible obs: 99.91 % / Redundancy: 1 % / CC1/2: 0.997 / Net I/σ(I): 2.2
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 107909 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 2.2→38.685 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 2000 1.85 %
Rwork0.1803 105927 -
obs0.1812 107927 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.79 Å2 / Biso mean: 43.2097 Å2 / Biso min: 17.35 Å2
Refinement stepCycle: final / Resolution: 2.2→38.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10928 0 16 805 11749
Biso mean--42.98 42.58 -
Num. residues----1311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.25490.27791410.20897475
2.2549-2.31580.2691420.20277538
2.3158-2.3840.2651410.19317490
2.384-2.46090.22551430.19487516
2.4609-2.54880.24121410.18777510
2.5488-2.65090.26231430.19947558
2.6509-2.77150.25221420.1997514
2.7715-2.91750.25061420.18977534
2.9175-3.10030.24581420.19177562
3.1003-3.33950.2561440.19197574
3.3395-3.67530.20091430.17187585
3.6753-4.20660.22011440.16567606
4.2066-5.29770.17371440.15227642

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