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- PDB-7xa4: Thermotoga maritima ferritin variant-Tm-E (S111H) with Zn -

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Basic information

Entry
Database: PDB / ID: 7xa4
TitleThermotoga maritima ferritin variant-Tm-E (S111H) with Zn
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / protein assembly
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / 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 ...Ferritin, prokaryotic-type / 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
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLiu, Y. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Nano / Year: 2022
Title: Directed Self-Assembly of Dimeric Building Blocks into Networklike Protein Origami to Construct Hydrogels.
Authors: Liu, Y. / Chen, X. / Yin, S. / Chang, X. / Lv, C. / Zang, J. / Leng, X. / Zhang, T. / Zhao, G.
History
DepositionMar 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 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)17,6163
Polymers17,4861
Non-polymers1312
Water41423
1
A: Ferritin
hetero molecules

A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2336
Polymers34,9712
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area2730 Å2
ΔGint-169 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.840, 55.840, 129.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Ferritin


Mass: 17485.652 Da / Num. of mol.: 1 / Mutation: S111H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Mes pH 6.0, 200mM Lithium sulfate, 2mM Zinc chloride, 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.276911 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.276911 Å / Relative weight: 1
ReflectionResolution: 1.96→32.19 Å / Num. obs: 33026 / % possible obs: 98.18 % / Redundancy: 2 % / CC1/2: 0.978 / Net I/σ(I): 10.06
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 3210 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vlg

1vlg


Resolution: 1.96→32.19 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 3158 9.95 %
Rwork0.2105 28569 -
obs0.213 31727 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.69 Å2 / Biso mean: 37.1498 Å2 / Biso min: 18.07 Å2
Refinement stepCycle: final / Resolution: 1.96→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 2 23 1224
Biso mean--40.75 36.63 -
Num. residues----143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.990.36241500.33981276142696
1.99-2.020.27931290.26411188131797
2.02-2.050.29611460.23791242138898
2.05-2.090.24641340.22031238137297
2.09-2.120.2271440.23291218136297
2.12-2.160.29611320.2251268140098
2.16-2.210.31351430.26151266140998
2.21-2.260.48361210.46481099122087
2.26-2.310.48141330.37971192132592
2.31-2.370.26981310.23931210134198
2.37-2.430.24751450.20961275142098
2.43-2.50.24331300.22261231136199
2.5-2.580.26131370.20791273141098
2.58-2.680.24581380.21681275141399
2.68-2.780.26491370.20911275141299
2.78-2.910.22171280.21851243137199
2.91-3.060.261410.22561266140799
3.06-3.250.24581430.21881242138599
3.26-3.50.21551420.20751283142599
3.5-3.860.22041370.19181227136497
3.86-4.410.18571370.16081249138698
4.42-5.550.16371410.15971273141499
5.56-32.190.19181390.17141260139999
Refinement TLS params.Method: refined / Origin x: -15.7269 Å / Origin y: -4.1798 Å / Origin z: 12.1142 Å
111213212223313233
T0.1835 Å20.0259 Å2-0.0161 Å2-0.2573 Å2-0.0137 Å2--0.2297 Å2
L0.8108 °2-0.3585 °20.3003 °2-2.8091 °2-0.4838 °2--1.7236 °2
S-0.0692 Å °-0.1592 Å °0.0504 Å °0.0378 Å °-0.0381 Å °0.023 Å °-0.0828 Å °-0.0908 Å °0.0991 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 145
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1 - 25

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