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- PDB-7die: Crystal structure of M. penetrans Ferritin -

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Basic information

Entry
Database: PDB / ID: 7die
TitleCrystal structure of M. penetrans Ferritin
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / Ferritin / Iron uptake / Iron release.
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 protein Rsg
Function and homology information
Biological speciesMycoplasma penetrans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWang, w.m. / Zhang, y. / Wang, h.f.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21601112, 21671125 China
CitationJournal: Inorg.Chem. / Year: 2021
Title: Ferritin with Atypical Ferroxidase Centers Takes B-Channels as the Pathway for Fe 2+ Uptake from Mycoplasma .
Authors: Wang, W. / Zhang, Y. / Zhao, G. / Wang, H.
History
DepositionNov 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,99242
Polymers123,9816
Non-polymers2,01036
Water13,313739
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)503,966168
Polymers495,92424
Non-polymers8,042144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area104660 Å2
ΔGint-2253 kcal/mol
Surface area123920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.334, 151.334, 125.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-203-

FE

21A-204-

FE

31A-205-

FE

41F-203-

FE

51F-204-

FE

61F-205-

FE

71F-207-

FE

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Components

#1: Protein
Ferritin


Mass: 20663.520 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma penetrans (strain HF-2) (bacteria)
Strain: HF-2 / Gene: MYPE2930 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EWB1, bacterial non-heme ferritin
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium acetate, 0.1 M Tris-HCl (pH 8.5), 10-15% (w/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 110615 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Χ2: 1.609 / Net I/σ(I): 30.79
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 3.875 / Num. unique obs: 5458 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.174 / Rrim(I) all: 0.463

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.856 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1772 2000 1.81 %
Rwork0.1531 108250 -
obs0.1536 110250 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.4 Å2 / Biso mean: 33.904 Å2 / Biso min: 21.17 Å2
Refinement stepCycle: final / Resolution: 1.9→47.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 36 739 8701
Biso mean--65.14 42.35 -
Num. residues----984
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9001-1.94760.24171400.1964765499
1.9476-2.00030.23881430.18697743100
2.0003-2.05920.22341440.17477709100
2.0592-2.12560.19191440.1649764699
2.1256-2.20160.20451430.16567729100
2.2016-2.28970.18861470.16197776100
2.2897-2.3940.2061380.16347722100
2.394-2.52020.20091460.16647760100
2.5202-2.6780.20341400.1554768299
2.678-2.88480.1911460.16247764100
2.8848-3.17510.16581420.15787774100
3.1751-3.63440.16611400.1442773299
3.6344-4.57830.15081390.13697796100
4.5783-100.15891480.1452776399

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