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- PDB-7pfb: 2 minute Fe2+ soaked structure of SynFtn Variant D65A -

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Basic information

Entry
Database: PDB / ID: 7pfb
Title2 minute Fe2+ soaked structure of SynFtn Variant D65A
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / iron binding protein
Function / homology
Function and homology information


bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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 speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Model detailsstructure determined from crystals of SynFtn D65A that have not been soaked in Fe2+
AuthorsHemmings, A.M. / Bradley, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R002363/1 United Kingdom
CitationJournal: Microbiology (Reading, Engl.) / Year: 2021
Title: Key carboxylate residues for iron transit through the prokaryotic ferritin Syn Ftn.
Authors: Bradley, J.M. / Fair, J. / Hemmings, A.M. / Le Brun, N.E.
History
DepositionAug 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4276
Polymers20,1881
Non-polymers2385
Water4,035224
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)490,243144
Polymers484,52024
Non-polymers5,723120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area103220 Å2
ΔGint-1333 kcal/mol
Surface area130460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.240, 177.240, 177.240
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-203-

FE

21A-204-

CL

31A-450-

HOH

41A-517-

HOH

51A-524-

HOH

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Components

#1: Protein Ferritin /


Mass: 20188.346 Da / Num. of mol.: 1 / Fragment: ferritin / Mutation: D65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria)
Strain: CC9311 / Gene: sync_1539 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0I9X8, bacterial non-heme ferritin
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.87 Å3/Da / Density % sol: 57.19 % / Mosaicity: 0 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.66→44.31 Å / Num. obs: 28740 / % possible obs: 100 % / Redundancy: 77.3 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.011 / Rrim(I) all: 0.093 / Net I/σ(I): 33.8 / Num. measured all: 2221649 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.66-1.778.23.82916279920830.7320.4343.8531.8100
7.43-44.3162.10.0362526440710.0040.037107.299.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 5OUW

5ouw


Resolution: 1.7→40.662 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 1341 5 %
Rwork0.1738 25471 -
obs0.1751 26812 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.24 Å2 / Biso mean: 30.8219 Å2 / Biso min: 21.14 Å2
Refinement stepCycle: final / Resolution: 1.7→40.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 5 224 1619
Biso mean--34.48 40.54 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061449
X-RAY DIFFRACTIONf_angle_d0.7081975
X-RAY DIFFRACTIONf_chiral_restr0.045221
X-RAY DIFFRACTIONf_plane_restr0.004264
X-RAY DIFFRACTIONf_dihedral_angle_d13.722889
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7001-1.76090.29421270.26222508
1.7609-1.83140.29441290.23892476
1.8314-1.91480.25871340.22372483
1.9148-2.01570.22671340.20882505
2.0157-2.1420.23821360.1932506
2.142-2.30740.2181310.18062511
2.3074-2.53950.17851410.18642534
2.5395-2.90690.18731230.1822567
2.9069-3.66210.19421420.1592589
3.6621-40.6620.18491440.15672792

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