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- PDB-7vp8: Crystal structure of ferritin from Ureaplasma urealyticum -

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Basic information

Entry
Database: PDB / ID: 7vp8
TitleCrystal structure of ferritin from Ureaplasma urealyticum
ComponentsFerritin-like diiron domain-containing protein
KeywordsMETAL BINDING PROTEIN / Ferritin / Ferritin subfamily / Ureaplasma / Mycoplasma
Function / homologyFerritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / ferric iron binding / Ferritin-like superfamily / : / Ferritin-like diiron domain-containing protein
Function and homology information
Biological speciesUreaplasma urealyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.002 Å
AuthorsWang, W. / Liu, X. / Wang, Y. / Fu, D. / Wang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118, 21601112 China
CitationJournal: Chin.Chem.Lett. / Year: 2022
Title: Distinct structural characteristics define a new subfamily of Mycoplasma ferritin
Authors: Wang, W. / Liu, X. / Wang, Y. / Wang, Y. / Fu, D. / Xi, H. / Zhao, Y. / Wang, H.
History
DepositionOct 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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-like diiron domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3778
Polymers20,0471
Non-polymers3307
Water4,143230
1
A: Ferritin-like diiron domain-containing protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)489,037192
Polymers481,12424
Non-polymers7,914168
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
Buried area103860 Å2
ΔGint-2011 kcal/mol
Surface area141790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.441, 178.441, 178.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-204-

FE

21A-454-

HOH

31A-469-

HOH

41A-473-

HOH

51A-495-

HOH

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Components

#1: Protein Ferritin-like diiron domain-containing protein


Mass: 20046.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureaplasma urealyticum (bacteria) / Gene: EPH05_02360 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A514J930
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: NaCl, PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→34.341 Å / Num. obs: 16992 / % possible obs: 100 % / Redundancy: 37.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Net I/σ(I): 42.6
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 9.37 / Num. unique obs: 832 / CC1/2: 0.976

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.002→34.341 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 1697 10 %
Rwork0.1591 15279 -
obs0.1623 16976 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.7 Å2 / Biso mean: 21.4593 Å2 / Biso min: 7.86 Å2
Refinement stepCycle: final / Resolution: 2.002→34.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 7 230 1618
Biso mean--46 28.99 -
Num. residues----168
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.002-2.06040.25851370.16371226
2.0604-2.12690.18881380.16111249
2.1269-2.20290.2061390.15411242
2.2029-2.29110.23311370.15251249
2.2911-2.39540.20521380.15781232
2.3954-2.52160.18581400.1621263
2.5216-2.67960.22461400.16721258
2.6796-2.88630.21591390.17831259
2.8863-3.17660.20751430.16611275
3.1766-3.63590.18431420.14941293
3.6359-4.57910.15121470.13341309
4.5791-34.3410.16091570.1761424

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