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- PDB-4ixk: Anaerobic crystal structure of iron soaked (2 h) ferritin from Ps... -

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Basic information

Entry
Database: PDB / ID: 4ixk
TitleAnaerobic crystal structure of iron soaked (2 h) 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: 2.1 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 26, 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)151,38316
Polymers150,9368
Non-polymers4478
Water9,440524
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)454,14848
Polymers452,80824
Non-polymers1,34024
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area70650 Å2
ΔGint-690 kcal/mol
Surface area135260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.323, 174.323, 174.323
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
11A-304-

HOH

21A-352-

HOH

31D-304-

HOH

41B-304-

HOH

51B-313-

HOH

61B-371-

HOH

71H-346-

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.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5 / Details: pH 5.5, VAPOR DIFFUSION, SITTING 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: 2.1→50 Å / Num. obs: 102638 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.084 / Χ2: 1.092 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1414.60.59750591.1841100
2.14-2.1814.70.53350661.1761100
2.18-2.2214.70.43351121.1571100
2.22-2.2614.70.3951291.1661100
2.26-2.3114.70.3550841.1791100
2.31-2.3714.70.31550871.1641100
2.37-2.4214.70.26750951.1691100
2.42-2.4914.70.22651371.1621100
2.49-2.5614.80.250691.1361100
2.56-2.6514.70.18151331.1431100
2.65-2.7414.80.1551241.1481100
2.74-2.8514.80.1350961.1181100
2.85-2.9814.80.11451341.1021100
2.98-3.1414.70.10351170.9261100
3.14-3.3314.60.09251460.9081100
3.33-3.5914.40.07851130.8821100
3.59-3.9514.40.06651740.9081100
3.95-4.5214.20.04351761.0251100
4.52-5.714.80.03352241.0921100
5.7-5014.60.03153631.091199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å48.35 Å
Translation2.1 Å48.35 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: 2.1→48.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2526 / WRfactor Rwork: 0.2095 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8074 / SU B: 4.274 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1888 / SU Rfree: 0.1748 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 5096 5 %RANDOM
Rwork0.2006 ---
obs0.203 102117 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.19 Å2 / Biso mean: 32.8978 Å2 / Biso min: 10.41 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9938 0 8 524 10470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910288
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9414044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16651297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.28425.712541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.628151686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6321548
X-RAY DIFFRACTIONr_chiral_restr0.1330.21569
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218036
X-RAY DIFFRACTIONr_mcbond_it2.9222.9815065
X-RAY DIFFRACTIONr_mcangle_it3.7184.446334
X-RAY DIFFRACTIONr_scbond_it4.7423.425219
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 354 -
Rwork0.213 7144 -
all-7498 -
obs--99.81 %

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