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- PDB-4iwj: Crystal structure of iron soaked (45 min) ferritin from Pseudo-ni... -

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Basic information

Entry
Database: PDB / ID: 4iwj
TitleCrystal structure of iron soaked (45 min) ferritin from Pseudo-nitzschia multiseries
ComponentsFerritin
KeywordsTRANSPORT PROTEIN / ferritin / 4 helix bundle / iron storage / acetamido-cysteines
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudo-nitzschia multiseries (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsPfaffen, S. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Mechanism of ferrous iron binding and oxidation by ferritin from a pennate diatom.
Authors: Pfaffen, S. / Abdulqadir, R. / Le Brun, N.E. / Murphy, M.E.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,82924
Polymers150,9368
Non-polymers89416
Water18,1231006
1
A: Ferritin
D: Ferritin
B: Ferritin
C: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)455,48872
Polymers452,80824
Non-polymers2,68148
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area67750 Å2
ΔGint-390 kcal/mol
Surface area135140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.319, 175.319, 175.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

21B-418-

HOH

31B-420-

HOH

41C-323-

HOH

51H-331-

HOH

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Components

#1: Protein
Ferritin


Mass: 18866.980 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudo-nitzschia multiseries (Diatom) / Gene: FTN / Production host: Escherichia coli (E. coli) / References: UniProt: B6DMH6
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5 / Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 129748 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.064 / Χ2: 1.086 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.0270.528128041.0321100
2.02-2.17.80.364129111.1951100
2.1-2.28.90.25129121.1041100
2.2-2.3110.30.186129011.1431100
2.31-2.4611.70.143129101.0771100
2.46-2.6512.90.109129711.1431100
2.65-2.9113.80.077129511.1131100
2.91-3.3314.30.066130051.0321100
3.33-4.214.30.056130770.9451100
4.2-5014.30.027133061.131199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å41.33 Å
Translation1.95 Å41.33 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→41.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2058 / WRfactor Rwork: 0.1697 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8539 / SU B: 2.775 / SU ML: 0.081 / SU R Cruickshank DPI: 0.132 / SU Rfree: 0.1293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 6480 5 %RANDOM
Rwork0.1729 ---
obs0.1749 128778 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.18 Å2 / Biso mean: 28.5277 Å2 / Biso min: 9.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10073 0 16 1006 11095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01910563
X-RAY DIFFRACTIONr_angle_refined_deg2.061.93814429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05451335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42825.582550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.722151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5231550
X-RAY DIFFRACTIONr_chiral_restr0.1640.21599
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218307
X-RAY DIFFRACTIONr_mcbond_it2.7232.4615229
X-RAY DIFFRACTIONr_mcangle_it3.4973.6616577
X-RAY DIFFRACTIONr_scbond_it4.9172.9525328
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 486 -
Rwork0.205 9006 -
all-9492 -
obs--99.78 %

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