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- PDB-7dyb: Thermotoga maritima ferritin mutant-FLAL-L -

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Basic information

Entry
Database: PDB / ID: 7dyb
TitleThermotoga maritima ferritin mutant-FLAL-L
ComponentsFerritin
KeywordsRECOMBINATION / Thermotoga maritima ferritin / assembly
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: 1.779 Å
AuthorsZhao, G. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31730069 China
CitationJournal: Nat Commun / Year: 2021
Title: Protein interface redesign facilitates the transformation of nanocage building blocks to 1D and 2D nanomaterials.
Authors: Zhang, X. / Liu, Y. / Zheng, B. / Zang, J. / Lv, C. / Zhang, T. / Wang, H. / Zhao, G.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2389
Polymers57,9033
Non-polymers3356
Water8,197455
1
H: Ferritin
hetero molecules

H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8256
Polymers38,6022
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2370 Å2
ΔGint-13 kcal/mol
Surface area16020 Å2
MethodPISA
2
A: Ferritin
B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8256
Polymers38,6022
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-10 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.343, 54.647, 59.910
Angle α, β, γ (deg.)90.000, 109.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ferritin


Mass: 19300.863 Da / Num. of mol.: 3 / Mutation: E112L, E113A, K114L, R137L, N147F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 200 mM NaCl, 20% PEG 3000 and 100 mM HEPES/NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.779→56.32 Å / Num. obs: 48748 / % possible obs: 94.64 % / Redundancy: 7.6 % / CC1/2: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 1.78→1.844 Å / Num. unique obs: 3604 / CC1/2: 0.965

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Processing

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

1vlg


Resolution: 1.779→56.317 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 2011 4.13 %
Rwork0.1941 46663 -
obs0.1958 48674 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.04 Å2 / Biso mean: 27.8364 Å2 / Biso min: 16.08 Å2
Refinement stepCycle: final / Resolution: 1.779→56.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 6 455 4520
Biso mean--26.07 35.01 -
Num. residues----489
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.779-1.82330.38411050.3037238568
1.8233-1.87260.29851180.2556275178
1.8726-1.92770.30041380.248308889
1.9277-1.98990.29411390.2169341397
1.9899-2.0610.26761500.2138346599
2.061-2.14360.2711520.1997348999
2.1436-2.24110.22331490.1825347699
2.2411-2.35930.25591490.1823350599
2.3593-2.50710.25321480.1903348299
2.5071-2.70070.24521520.20033509100
2.7007-2.97240.22061510.2009346899
2.9724-3.40250.23911540.1897353199
3.4025-4.28660.18361530.1719354599
4.2866-80.21661530.1851355698

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