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- PDB-5ls9: Humanized Archaeal ferritin -

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Basic information

Entry
Database: PDB / ID: 5ls9
TitleHumanized Archaeal ferritin
ComponentsFerritin, putative
KeywordsMETAL BINDING PROTEIN / chimeric protein ferritin metal binding protein
Function / homology
Function and homology information


intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / 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
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsBaiocco, P. / Trabuco, M.C. / Boffi, A.
CitationJournal: Nanoscale / Year: 2017
Title: Humanized archaeal ferritin as a tool for cell targeted delivery.
Authors: de Turris, V. / Cardoso Trabuco, M. / Peruzzi, G. / Boffi, A. / Testi, C. / Vallone, B. / Celeste Montemiglio, L. / Georges, A.D. / Calisti, L. / Benni, I. / Bonamore, A. / Baiocco, P.
History
DepositionAug 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin, putative
B: Ferritin, putative
C: Ferritin, putative
D: Ferritin, putative
E: Ferritin, putative
F: Ferritin, putative
G: Ferritin, putative
H: Ferritin, putative
I: Ferritin, putative
J: Ferritin, putative
K: Ferritin, putative
L: Ferritin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,81514
Polymers244,76612
Non-polymers492
Water23413
1
A: Ferritin, putative
B: Ferritin, putative
C: Ferritin, putative
D: Ferritin, putative
E: Ferritin, putative
F: Ferritin, putative
G: Ferritin, putative
H: Ferritin, putative
I: Ferritin, putative
J: Ferritin, putative
K: Ferritin, putative
L: Ferritin, putative
hetero molecules

A: Ferritin, putative
B: Ferritin, putative
C: Ferritin, putative
D: Ferritin, putative
E: Ferritin, putative
F: Ferritin, putative
G: Ferritin, putative
H: Ferritin, putative
I: Ferritin, putative
J: Ferritin, putative
K: Ferritin, putative
L: Ferritin, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)489,62928
Polymers489,53224
Non-polymers974
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)185.797, 190.650, 176.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 166
2114B3 - 166
3114C3 - 166
4114D3 - 166
5114E3 - 166
6114F3 - 166
7114G3 - 166
8114H3 - 166
9114I3 - 166
10114J3 - 166
11114K3 - 166
12114L3 - 166

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.996976, -0.022951, -0.074238), (-0.028078, -0.784431, 0.61958), (-0.072455, 0.619791, 0.781415)-96.16295, 5.65209, -5.89815
3given(0.032308, 0.719893, 0.693332), (-0.996692, 0.074963, -0.031392), (-0.074573, -0.690025, 0.719934)-40.4479, -47.49412, -6.52906
4given(0.000414, -0.643547, -0.765406), (0.736742, -0.517352, 0.435383), (-0.676174, -0.564087, 0.473914)-55.53174, 39.82359, -37.43767
5given(-0.005502, 0.747752, -0.663956), (-0.684297, -0.486975, -0.542764), (-0.729182, 0.451357, 0.514364)-53.95459, -35.99173, -39.46035
6given(0.076869, -0.766257, 0.637919), (0.091721, 0.642534, 0.760748), (-0.992813, 3.3E-5, 0.119672)-38.40041, 10.72198, -54.92027
7given(-0.9998, 0.016341, -0.011563), (-0.013491, -0.1233, 0.992278), (0.014789, 0.992235, 0.123495)-107.73722, -1.95239, 1.57635
8given(0.996052, -0.084903, -0.025917), (0.042469, 0.712138, -0.700754), (0.077952, 0.696887, 0.712932)11.30689, 10.57649, 1.87554
9given(-0.040063, 0.602009, 0.797484), (0.997963, -0.015545, 0.061868), (0.049642, 0.798338, -0.60016)-44.93353, 61.99559, 0.47197
10given(0.007346, -0.678865, -0.734226), (-0.739618, 0.490462, -0.460882), (0.672987, 0.546433, -0.498498)-54.47013, -40.16656, 36.65425
11given(-0.02034, -0.748531, 0.662788), (0.68983, -0.490356, -0.532622), (0.723686, 0.446377, 0.526333)-56.40818, 38.5731, 38.6942
12given(-0.054979, 0.723098, -0.688554), (-0.117011, 0.68018, 0.723646), (0.991608, 0.120354, 0.047215)-44.19822, -1.95017, 52.65534

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Components

#1: Protein
Ferritin, putative


Mass: 20397.174 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0834 / Production host: Escherichia coli (E. coli) / References: UniProt: O29424
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 22% Polyacrylic acid Tris pH 7.4 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87292 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87292 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.846
11K, H, -L20.154
ReflectionResolution: 2.93→50 Å / Num. obs: 59926 / % possible obs: 96 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.8
Reflection shellResolution: 2.93→3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.8 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3Q

1s3q


Resolution: 2.93→49.69 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.835 / SU B: 23.569 / SU ML: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3019 3071 5.1 %RANDOM
Rwork0.2771 ---
obs0.2784 56823 89.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.88 Å2 / Biso mean: 70.446 Å2 / Biso min: 24.81 Å2
Baniso -1Baniso -2Baniso -3
1-28.25 Å20 Å20 Å2
2---19.7 Å20 Å2
3----8.55 Å2
Refinement stepCycle: final / Resolution: 2.93→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16335 0 2 13 16350
Biso mean--58.26 40.17 -
Num. residues----1963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01916695
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215673
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.94322473
X-RAY DIFFRACTIONr_angle_other_deg0.719336051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38551951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89624.538899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93153099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2341596
X-RAY DIFFRACTIONr_chiral_restr0.0530.22363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024033
X-RAY DIFFRACTIONr_mcbond_it2.7657.0147840
X-RAY DIFFRACTIONr_mcbond_other2.7657.0147839
X-RAY DIFFRACTIONr_mcangle_it4.57710.5189779
Refine LS restraints NCS

Ens-ID: 1 / Number: 2638 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.610.5
2BMEDIUM POSITIONAL0.550.5
3CMEDIUM POSITIONAL0.580.5
4DMEDIUM POSITIONAL0.540.5
5EMEDIUM POSITIONAL0.540.5
6FMEDIUM POSITIONAL0.50.5
7GMEDIUM POSITIONAL0.580.5
8HMEDIUM POSITIONAL0.650.5
9IMEDIUM POSITIONAL0.550.5
10JMEDIUM POSITIONAL0.510.5
11AMEDIUM POSITIONAL0.630.5
12BMEDIUM POSITIONAL0.590.5
1AMEDIUM THERMAL12.262
2BMEDIUM THERMAL16.192
3CMEDIUM THERMAL15.212
4DMEDIUM THERMAL10.632
5EMEDIUM THERMAL10.92
6FMEDIUM THERMAL9.412
7GMEDIUM THERMAL11.342
8HMEDIUM THERMAL14.062
9IMEDIUM THERMAL10.282
10JMEDIUM THERMAL17.132
11AMEDIUM THERMAL10.042
12BMEDIUM THERMAL17.232
LS refinement shellResolution: 2.932→3.008 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.593 20 -
Rwork0.712 346 -
all-366 -
obs--7.45 %

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