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- PDB-6txh: Crystal structure of thermotoga maritima Ferritin in apo form -

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Basic information

Entry
Database: PDB / ID: 6txh
TitleCrystal structure of thermotoga maritima Ferritin in apo form
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Metal binding / engineered protein
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 / 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 / molecular replacement / Resolution: 2.198 Å
AuthorsWilk, P. / Grudnik, P. / Kumar, M. / Heddle, J. / Chakraborti, S.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish ScienceHoming/2017-3/22 Poland
CitationJournal: Nanoscale / Year: 2021
Title: A single residue can modulate nanocage assembly in salt dependent ferritin.
Authors: Kumar, M. / Markiewicz-Mizera, J. / Janna Olmos, J.D. / Wilk, P. / Grudnik, P. / Biela, A.P. / Jemiola-Rzeminska, M. / Gorecki, A. / Chakraborti, S. / Heddle, J.G.
History
DepositionJan 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)159,11941
Polymers155,2158
Non-polymers3,90433
Water6,377354
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,356123
Polymers465,64424
Non-polymers11,71299
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area98700 Å2
ΔGint-1148 kcal/mol
Surface area148990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.172, 176.172, 351.708
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 17 or resid 19...
21(chain C and (resid 2 through 17 or resid 19...
31(chain D and (resid 2 through 17 or resid 19...
41(chain E and (resid 2 through 17 or resid 19...
51(chain F and (resid 2 through 17 or resid 19...
61(chain G and (resid 2 through 17 or resid 19...
71(chain H and (resid 2 through 17 or resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 17 or resid 19...A2 - 17
121(chain A and (resid 2 through 17 or resid 19...A19 - 21
131(chain A and (resid 2 through 17 or resid 19...A1 - 164
141(chain A and (resid 2 through 17 or resid 19...A0
151(chain A and (resid 2 through 17 or resid 19...A51 - 68
161(chain A and (resid 2 through 17 or resid 19...A70 - 86
171(chain A and (resid 2 through 17 or resid 19...A88 - 111
181(chain A and (resid 2 through 17 or resid 19...A114 - 122
191(chain A and (resid 2 through 17 or resid 19...A124 - 131
1101(chain A and (resid 2 through 17 or resid 19...A133 - 134
1111(chain A and (resid 2 through 17 or resid 19...A136 - 157
1121(chain A and (resid 2 through 17 or resid 19...A159 - 161
1131(chain A and (resid 2 through 17 or resid 19...A163 - 164
211(chain C and (resid 2 through 17 or resid 19...C2 - 17
221(chain C and (resid 2 through 17 or resid 19...C19 - 21
231(chain C and (resid 2 through 17 or resid 19...C1 - 164
241(chain C and (resid 2 through 17 or resid 19...C1 - 164
251(chain C and (resid 2 through 17 or resid 19...C70 - 86
261(chain C and (resid 2 through 17 or resid 19...C88 - 111
271(chain C and (resid 2 through 17 or resid 19...C0
281(chain C and (resid 2 through 17 or resid 19...C133 - 134
291(chain C and (resid 2 through 17 or resid 19...C157
2101(chain C and (resid 2 through 17 or resid 19...C159 - 161
2111(chain C and (resid 2 through 17 or resid 19...C159 - 161
2121(chain C and (resid 2 through 17 or resid 19...C163 - 164
311(chain D and (resid 2 through 17 or resid 19...D2 - 17
321(chain D and (resid 2 through 17 or resid 19...D19 - 21
331(chain D and (resid 2 through 17 or resid 19...D23 - 27
341(chain D and (resid 2 through 17 or resid 19...D1 - 68
351(chain D and (resid 2 through 17 or resid 19...D70 - 86
361(chain D and (resid 2 through 17 or resid 19...D1 - 164
371(chain D and (resid 2 through 17 or resid 19...D1 - 164
381(chain D and (resid 2 through 17 or resid 19...D124 - 131
391(chain D and (resid 2 through 17 or resid 19...D159 - 161
3101(chain D and (resid 2 through 17 or resid 19...D163 - 164
411(chain E and (resid 2 through 17 or resid 19...E2 - 17
421(chain E and (resid 2 through 17 or resid 19...E19 - 21
431(chain E and (resid 2 through 17 or resid 19...E23 - 27
441(chain E and (resid 2 through 17 or resid 19...E29 - 49
451(chain E and (resid 2 through 17 or resid 19...E51 - 68
461(chain E and (resid 2 through 17 or resid 19...E70 - 86
471(chain E and (resid 2 through 17 or resid 19...E88 - 111
481(chain E and (resid 2 through 17 or resid 19...E114 - 122
491(chain E and (resid 2 through 17 or resid 19...E124 - 131
4101(chain E and (resid 2 through 17 or resid 19...E133 - 134
4111(chain E and (resid 2 through 17 or resid 19...E136 - 157
4121(chain E and (resid 2 through 17 or resid 19...E159 - 161
4131(chain E and (resid 2 through 17 or resid 19...E163 - 164
511(chain F and (resid 2 through 17 or resid 19...F2 - 17
521(chain F and (resid 2 through 17 or resid 19...F19 - 21
531(chain F and (resid 2 through 17 or resid 19...F23 - 27
541(chain F and (resid 2 through 17 or resid 19...F29 - 49
551(chain F and (resid 2 through 17 or resid 19...F70 - 86
561(chain F and (resid 2 through 17 or resid 19...F1 - 164
571(chain F and (resid 2 through 17 or resid 19...F1 - 164
581(chain F and (resid 2 through 17 or resid 19...F133 - 134
591(chain F and (resid 2 through 17 or resid 19...F136 - 157
5101(chain F and (resid 2 through 17 or resid 19...F159 - 161
5111(chain F and (resid 2 through 17 or resid 19...F163 - 164
611(chain G and (resid 2 through 17 or resid 19...G2 - 17
621(chain G and (resid 2 through 17 or resid 19...G19 - 21
631(chain G and (resid 2 through 17 or resid 19...G1 - 164
641(chain G and (resid 2 through 17 or resid 19...G1 - 164
651(chain G and (resid 2 through 17 or resid 19...G70 - 86
661(chain G and (resid 2 through 17 or resid 19...G88 - 111
671(chain G and (resid 2 through 17 or resid 19...G0
681(chain G and (resid 2 through 17 or resid 19...G133 - 134
691(chain G and (resid 2 through 17 or resid 19...G157
6101(chain G and (resid 2 through 17 or resid 19...G159 - 161
6111(chain G and (resid 2 through 17 or resid 19...G159 - 161
6121(chain G and (resid 2 through 17 or resid 19...G163 - 164
711(chain H and (resid 2 through 17 or resid 19...H2 - 17
721(chain H and (resid 2 through 17 or resid 19...H19 - 21
731(chain H and (resid 2 through 17 or resid 19...H1 - 164
741(chain H and (resid 2 through 17 or resid 19...H1 - 164
751(chain H and (resid 2 through 17 or resid 19...H70 - 86
761(chain H and (resid 2 through 17 or resid 19...H88 - 111
771(chain H and (resid 2 through 17 or resid 19...H0
781(chain H and (resid 2 through 17 or resid 19...H133 - 134
791(chain H and (resid 2 through 17 or resid 19...H157
7101(chain H and (resid 2 through 17 or resid 19...H159 - 161
7111(chain H and (resid 2 through 17 or resid 19...H159 - 161
7121(chain H and (resid 2 through 17 or resid 19...H163 - 164

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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 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: TM_1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0L2, bacterial non-heme ferritin
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H42
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2 M MgCl2, 2.4 M (NH4)2 SO4, 0.1M MES. pH 6.0. 1ul of 10mg/mL protein was mixed with same amount of well solution, crystals normally appears in 2 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Apr 13, 2019
RadiationMonochromator: Double Crystal Monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.198→25.068 Å / Num. obs: 106131 / % possible obs: 99.6 % / Redundancy: 10.189 % / Biso Wilson estimate: 61.486 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.128 / Χ2: 1.178 / Net I/σ(I): 13.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.3310.353.3910.6317432717078168430.3863.56898.6
2.33-2.4910.4541.891.1316738416058160120.571.98899.7
2.49-2.699.611.0612.0314351614968149340.7781.12299.8
2.69-2.959.980.54.3613736013808137640.9450.52799.7
2.95-3.2910.860.2329.9713571812506124970.9880.24399.9
3.29-3.810.5110.10322.5711644611086110780.9970.10999.9
3.8-4.659.7880.05837.3592146943094140.9990.06199.8
4.65-6.549.4990.04545.2269750737173430.9990.04899.6
6.54-25.06810.5330.03162.12447234268424610.03299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.58 Å48.81 Å
Translation7.58 Å48.81 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASER2.8.2phasing
PHENIX1.15.1_3469refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vlg

1vlg


Resolution: 2.198→25.068 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 35.32
RfactorNum. reflection% reflection
Rfree0.2343 2069 1.98 %
Rwork0.2044 --
obs0.205 104514 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.37 Å2 / Biso mean: 76.9256 Å2 / Biso min: 46.79 Å2
Refinement stepCycle: final / Resolution: 2.198→25.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10936 0 228 354 11518
Biso mean--97.61 74.37 -
Num. residues----1312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4945X-RAY DIFFRACTION12.103TORSIONAL
12C4945X-RAY DIFFRACTION12.103TORSIONAL
13D4945X-RAY DIFFRACTION12.103TORSIONAL
14E4945X-RAY DIFFRACTION12.103TORSIONAL
15F4945X-RAY DIFFRACTION12.103TORSIONAL
16G4945X-RAY DIFFRACTION12.103TORSIONAL
17H4945X-RAY DIFFRACTION12.103TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.198-2.24880.44941190.462585585
2.2488-2.3050.49191270.4664631492
2.305-2.36730.35381390.35936871100
2.3673-2.43690.36371390.34386850100
2.4369-2.51550.35781400.32176911100
2.5155-2.60530.33321390.29986893100
2.6053-2.70950.34911390.30056874100
2.7095-2.83260.35681390.26796915100
2.8326-2.98170.26911410.24486953100
2.9817-3.16820.30061390.24636921100
3.1682-3.41230.26091410.22636946100
3.4123-3.75470.22641410.19936975100
3.7547-4.29560.2181410.17396994100
4.2956-5.40310.14751410.1515699599
5.4031-25.0680.1921440.1582717899

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