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- PDB-2x17: The X-ray structure of Ferritin from Pyrococcus furiosus loaded w... -

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Basic information

Entry
Database: PDB / ID: 2x17
TitleThe X-ray structure of Ferritin from Pyrococcus furiosus loaded with Ag(I)
ComponentsPUTATIVE FERRITIN HOMOLOG
KeywordsMETAL TRANSPORT / FERRITIN / NANO-PARTICLES
Function / homology
Function and homology information


intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol
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
SILVER ION / Ferritin homolog
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsIlari, A. / Fiorillo, A. / Ceci, P.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Silver Ion Incorporation and Nanoparticle Formation Inside the Cavity of Pyrococcus Furiosus Ferritin: Structural and Size-Distribution Analyses.
Authors: Kasyutich, O. / Ilari, A. / Fiorillo, A. / Tatchev, D. / Hoell, A. / Ceci, P.
History
DepositionDec 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: PUTATIVE FERRITIN HOMOLOG
1: PUTATIVE FERRITIN HOMOLOG
2: PUTATIVE FERRITIN HOMOLOG
3: PUTATIVE FERRITIN HOMOLOG
4: PUTATIVE FERRITIN HOMOLOG
5: PUTATIVE FERRITIN HOMOLOG
6: PUTATIVE FERRITIN HOMOLOG
7: PUTATIVE FERRITIN HOMOLOG
8: PUTATIVE FERRITIN HOMOLOG
9: PUTATIVE FERRITIN HOMOLOG
G: PUTATIVE FERRITIN HOMOLOG
H: PUTATIVE FERRITIN HOMOLOG
I: PUTATIVE FERRITIN HOMOLOG
J: PUTATIVE FERRITIN HOMOLOG
K: PUTATIVE FERRITIN HOMOLOG
L: PUTATIVE FERRITIN HOMOLOG
M: PUTATIVE FERRITIN HOMOLOG
N: PUTATIVE FERRITIN HOMOLOG
O: PUTATIVE FERRITIN HOMOLOG
P: PUTATIVE FERRITIN HOMOLOG
Q: PUTATIVE FERRITIN HOMOLOG
R: PUTATIVE FERRITIN HOMOLOG
Y: PUTATIVE FERRITIN HOMOLOG
Z: PUTATIVE FERRITIN HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,45657
Polymers484,89624
Non-polymers3,56033
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area96280 Å2
ΔGint-740.43 kcal/mol
Surface area160000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.681, 157.681, 246.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
110
211
312
413
514
615
716
817
918
1019
111G
121H
131I
141J
151K
161L
171N
181M
191O
201P
211Q
221R
231Y
241Z

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
111401 - 172
211411 - 172
311421 - 172
411431 - 172
511441 - 172
611451 - 172
711461 - 172
811471 - 172
911481 - 172
1011491 - 172
11114G1 - 172
12114H1 - 172
13114I1 - 172
14114J1 - 172
15114K1 - 172
16114L1 - 172
18114M1 - 172
17114N1 - 172
19114O1 - 172
20114P1 - 172
21114Q1 - 172
22114R1 - 172
23114Y1 - 172
24114Z1 - 172

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.31103, -0.93871, -0.14863), (0.56886, -0.30916, 0.76211), (-0.76135, 0.15249, 0.63015)-98.62795, 46.60053, -58.50684
3given(-0.99604, 0.08525, 0.02527), (0.0846, 0.82128, 0.56421), (0.02734, 0.56411, -0.82524)-153.30264, 6.96138, 0.6066
4given(-0.25306, 0.91346, 0.31867), (0.00445, 0.33048, -0.9438), (-0.96744, -0.23742, -0.0877)-98.06266, 1.18408, -73.47054
5given(-0.25211, -0.00235, -0.9677), (0.90699, 0.34805, -0.23714), (0.33736, -0.93747, -0.08561)-96.21474, 70.99603, 27.7325
6given(0.33961, 0.01005, 0.94051), (0.91145, -0.25039, -0.32644), (0.23221, 0.96809, -0.0942)-50.06402, 72.68034, 15.87706
7given(0.81291, 0.08276, -0.57648), (0.09173, -0.99569, -0.0136), (-0.57512, -0.04183, -0.817)-14.89422, 11.54774, -44.19554
8given(0.22295, -0.88229, -0.41455), (-0.57045, 0.22676, -0.78941), (0.7905, 0.41248, -0.45274)-57.51031, -41.70454, 59.20051
9given(-0.82249, -0.1805, 0.53938), (-0.17578, -0.82122, -0.54287), (0.54093, -0.54131, 0.64372)-139.26711, -9.41528, 42.63627
10given(0.3395, 0.91035, 0.23663), (0.00953, -0.25489, 0.96692), (0.94056, -0.32602, -0.09521)-52.62653, 3.28637, 72.72798
11given(0.0064, -0.2536, 0.96729), (0.33724, 0.91119, 0.23666), (-0.9414, 0.32469, 0.09136)-75.67312, 26.15024, -72.88909
12given(0.00335, 0.3314, -0.94348), (-0.25378, 0.91288, 0.31975), (0.96726, 0.23837, 0.08716)-77.69582, -19.26122, 73.49255
13given(-0.1764, -0.82112, -0.54281), (-0.82188, -0.1806, 0.54028), (-0.54166, 0.54143, -0.64301)-88.29765, -60.38178, -42.66244
14given(0.9066, 0.34921, -0.2369), (-0.25209, -0.00201, -0.9677), (-0.33841, 0.93704, 0.08621)-7.8162, -17.36225, -27.78795
15given(0.08308, 0.81896, 0.5678), (-0.99625, 0.08201, 0.02749), (-0.02405, -0.56796, 0.82271)-72.01357, -74.57189, -0.61
16given(-0.88232, 0.20937, 0.42153), (0.23891, -0.57241, 0.78439), (0.40551, 0.79279, 0.45502)-144.84595, 21.23711, 29.85652
17given(0.56849, -0.30779, 0.76294), (-0.31319, -0.93852, -0.14525), (0.76074, -0.15637, -0.62993)-32.22578, -19.83797, 58.34291
18given(-0.5686, 0.22584, -0.79101), (0.2253, -0.88205, -0.41379), (-0.79116, -0.4135, 0.45065)-120.50104, 21.48301, -59.30031
19given(0.09219, -0.99555, -0.01956), (0.81299, 0.08659, -0.57581), (0.57494, 0.03718, 0.81735)-67.31162, 64.10123, 43.98989
20given(0.91174, -0.25215, -0.32427), (0.33796, 0.01176, 0.94109), (-0.23348, -0.96762, 0.09594)-6.19655, 28.75239, -15.91002
21given(-0.00015, 1, 0.00065), (1, 0.00015, 0.00049), (0.00049, 0.00065, -1)-78.84122, 78.86416, 0.05239
22given(-0.93413, -0.3205, 0.15709), (-0.32019, 0.55801, -0.76557), (0.15771, -0.76544, -0.62388)-147.80771, -23.91688, 13.50707
23given(-0.31866, 0.56063, -0.7643), (-0.93494, -0.31866, 0.15605), (-0.15606, 0.7643, 0.6257)-102.58054, -68.91823, -13.46304
24given(0.2397, -0.57182, 0.78458), (-0.8824, 0.2087, 0.42169), (-0.40487, -0.79339, -0.45455)-57.54787, -66.01788, -29.84276

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Components

#1: Protein ...
PUTATIVE FERRITIN HOMOLOG / SILVER LOADED FERRITIN FROM PYROCOCCUS FURIOSUS


Mass: 20204.008 Da / Num. of mol.: 24 / Fragment: RESIDUES 1-173
Source method: isolated from a genetically manipulated source
Details: FERRITIN LOADED WITH AG (I) / Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PET-11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U2T8
#2: Chemical...
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.4 Å3/Da / Density % sol: 63.8 % / Description: NONE
Crystal growpH: 7.5 / Details: 2.1-2.3 M AMMONIUM SULFATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: RAYONIX / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 107788 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 65.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JD6

2jd6


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.323 / SU ML: 0.444 / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28338 5386 5 %RANDOM
Rwork0.26014 ---
obs0.26132 102347 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.616 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20 Å2
2--3.01 Å20 Å2
3----6.01 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33983 0 33 26 34042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02234842
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7441.97846841
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.83754086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10824.7861795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.148156444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5815168
X-RAY DIFFRACTIONr_chiral_restr0.0440.24795
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02126572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1781.520563
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.332232727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.362314279
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4664.514114
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1407 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
10medium positional0.20.5
21medium positional0.220.5
32medium positional0.180.5
43medium positional0.190.5
54medium positional0.170.5
65medium positional0.190.5
76medium positional0.390.5
87medium positional0.210.5
98medium positional0.170.5
109medium positional0.190.5
11Gmedium positional0.310.5
12Hmedium positional0.170.5
13Imedium positional0.160.5
14Jmedium positional0.180.5
15Kmedium positional0.250.5
16Lmedium positional0.260.5
18Mmedium positional0.240.5
17Nmedium positional0.280.5
19Omedium positional0.240.5
20Pmedium positional0.160.5
21Qmedium positional0.150.5
22Rmedium positional0.20.5
23Ymedium positional0.170.5
24Zmedium positional0.230.5
10medium thermal0.042
21medium thermal0.042
32medium thermal0.062
43medium thermal0.042
54medium thermal0.042
65medium thermal0.052
76medium thermal0.052
87medium thermal0.042
98medium thermal0.042
109medium thermal0.052
11Gmedium thermal0.052
12Hmedium thermal0.052
13Imedium thermal0.052
14Jmedium thermal0.042
15Kmedium thermal0.062
16Lmedium thermal0.042
18Mmedium thermal0.052
17Nmedium thermal0.052
19Omedium thermal0.072
20Pmedium thermal0.052
21Qmedium thermal0.052
22Rmedium thermal0.042
23Ymedium thermal0.052
24Zmedium thermal0.062
LS refinement shellResolution: 3.097→3.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 409 -
Rwork0.328 7348 -
obs--96.65 %

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