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- PDB-7xa2: Thermotoga maritima ferritin variant-Tm-E(S111H) -

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Basic information

Entry
Database: PDB / ID: 7xa2
TitleThermotoga maritima ferritin variant-Tm-E(S111H)
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / protein assembly
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / cytosol / cytoplasm
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: 1.84 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 16, 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)17,5412
Polymers17,4861
Non-polymers561
Water28816
1
A: Ferritin
hetero molecules

A: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0834
Polymers34,9712
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area2610 Å2
ΔGint-39 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.490, 55.490, 129.070
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Mes pH 6.0, 200mM Lithium sulfate, 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.2769 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2769 Å / Relative weight: 1
ReflectionResolution: 1.84→44 Å / Num. obs: 39447 / % possible obs: 98.19 % / Redundancy: 2 % / CC1/2: 0.974 / Net I/σ(I): 15.94
Reflection shellResolution: 1.84→1.906 Å / Num. unique obs: 3623 / CC1/2: 0.423

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vlg

1vlg


Resolution: 1.84→43.02 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 3788 10.08 %
Rwork0.2072 33780 -
obs0.2089 37568 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.08 Å2 / Biso mean: 43.3944 Å2 / Biso min: 24.19 Å2
Refinement stepCycle: final / Resolution: 1.84→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 1 16 1216
Biso mean--102.08 39.21 -
Num. residues----143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.860.46581120.4695941105373
1.86-1.890.44631270.41361087121485
1.89-1.910.41651320.38471264139695
1.91-1.940.38331400.36461177131797
1.94-1.970.40891380.33381266140497
1.97-20.3591410.2991273141497
2-2.030.2811380.27881251138998
2.03-2.070.29661390.25291271141098
2.07-2.110.27831370.25411263140098
2.11-2.150.28371360.24871279141599
2.15-2.190.26181520.221254140699
2.19-2.240.22511440.22191285142999
2.24-2.290.2361460.20561271141799
2.29-2.350.26921310.2091249138099
2.35-2.410.23161500.20421316146699
2.41-2.480.23021320.20491235136799
2.48-2.560.24661450.20841288143399
2.56-2.650.26571420.2061276141899
2.65-2.760.26791460.204712971443100
2.76-2.890.26451310.207512831414100
2.89-3.040.22061480.203812581406100
3.04-3.230.2691460.213712951441100
3.23-3.480.1881500.208412891439100
3.48-3.830.18381480.190812701418100
3.83-4.380.16431420.176212861428100
4.38-5.520.17811520.179312901442100
5.52-43.020.20811430.18421266140999
Refinement TLS params.Method: refined / Origin x: -15.2487 Å / Origin y: -4.1238 Å / Origin z: 12.0276 Å
111213212223313233
T0.3113 Å20.0892 Å2-0.0187 Å2-0.3057 Å2-0.0111 Å2--0.3106 Å2
L0.1875 °2-0.0247 °20.3751 °2-0.3061 °20.0119 °2--0.7496 °2
S-0.1122 Å °-0.1424 Å °0.0275 Å °0.0301 Å °-0.0887 Å °-0.0114 Å °-0.1269 Å °-0.0786 Å °-0.0069 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 145
2X-RAY DIFFRACTION1allB1 - 16
3X-RAY DIFFRACTION1allC1

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