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- PDB-6hui: The structure of Dps from Listeria innocua soaked with zinc -

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Basic information

Entry
Database: PDB / ID: 6hui
TitleThe structure of Dps from Listeria innocua soaked with zinc
ComponentsDNA protection during starvation protein
KeywordsMETAL BINDING PROTEIN / Dps / metal binding. cage shaped protein / ferroxidase / itron translocation
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA protection during starvation protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å
AuthorsZeth, K. / Okuda, M.
CitationJournal: Inorg.Chem. / Year: 2019
Title: Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps.
Authors: Zeth, K. / Sancho-Vaello, E. / Okuda, M.
History
DepositionOct 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,47968
Polymers108,4236
Non-polymers4,05562
Water0
1
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
hetero molecules

A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,957136
Polymers216,84712
Non-polymers8,111124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)86.330, 86.330, 269.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
DNA protection during starvation protein / Ferritin-like protein / Non-heme iron-containing ferritin


Mass: 18070.553 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: dps, flp, fri, lin0942 / Production host: Escherichia coli (E. coli)
References: UniProt: P80725, Oxidoreductases; Oxidizing metal ions
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 62 / Source method: obtained synthetically / Formula: Zn

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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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG-3350, 100 mM Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.995→45.696 Å / Num. obs: 38906 / % possible obs: 99.6 % / Redundancy: 8.6 % / Net I/σ(I): 14.8
Reflection shellResolution: 2.995→3.18 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.995→45.696 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 35.04
RfactorNum. reflection% reflection
Rfree0.284 1949 5.01 %
Rwork0.2284 --
obs0.2311 38906 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.995→45.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7336 0 62 0 7398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027497
X-RAY DIFFRACTIONf_angle_d0.40310106
X-RAY DIFFRACTIONf_dihedral_angle_d10.5064476
X-RAY DIFFRACTIONf_chiral_restr0.0321097
X-RAY DIFFRACTIONf_plane_restr0.0031303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9954-3.07030.42241390.40042581X-RAY DIFFRACTION97
3.0703-3.15330.37951380.38982609X-RAY DIFFRACTION100
3.1533-3.2460.38571380.38342677X-RAY DIFFRACTION100
3.246-3.35080.40631380.36192621X-RAY DIFFRACTION100
3.3508-3.47050.33951450.34122664X-RAY DIFFRACTION100
3.4705-3.60940.34111380.30612664X-RAY DIFFRACTION100
3.6094-3.77360.34521320.30432642X-RAY DIFFRACTION100
3.7736-3.97250.4241360.28962650X-RAY DIFFRACTION100
3.9725-4.22120.31631420.25072657X-RAY DIFFRACTION100
4.2212-4.54680.28791500.2242659X-RAY DIFFRACTION100
4.5468-5.00390.26651310.19542642X-RAY DIFFRACTION100
5.0039-5.72680.30161370.21822664X-RAY DIFFRACTION100
5.7268-7.21050.26111410.1992651X-RAY DIFFRACTION100
7.2105-45.70110.18451440.14782576X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4071-0.792-1.86153.22321.15257.0126-0.643-1.00580.02261.19650.7699-0.4704-0.20821.0663-0.09911.3775-0.1274-0.55531.53740.39451.004726.5739-7.527620.9939
25.2887-2.1354-3.91724.49943.45463.8765-0.42150.4934-0.32680.1664-0.2972-0.4216-1.24170.20890.57461.3898-0.0769-0.48521.54330.43930.884421.7491-4.82714.3591
33.1138-1.1954-0.48643.09740.67411.2764-0.82120.17320.59680.80060.1324-0.9534-0.27371.6450.19881.4371-0.2885-0.66541.9190.38871.331232.6273-4.146117.6642
41.8128-0.0372-0.94984.86720.87960.69370.48340.5489-0.5259-0.9456-1.2851-0.74761.00431.60610.76741.30730.1346-0.00122.7270.4320.771822.7311-16.1308-18.5992
57.83035.2015-6.56375.415-4.49335.54171.05751.78740.34140.6188-0.6720.0807-0.13041.352-0.4021.05870.0093-0.09061.9870.45010.814619.0396-10.2353-13.0546
64.41990.589-1.13912.2688-2.46266.38430.62141.7672-0.4363-0.7825-0.8015-0.78860.76542.49760.72331.32850.73690.1282.60440.1571.024628.3513-17.3856-18.5512
79.62826.3524-3.39124.924-0.09597.39450.78271.5883-0.22440.3069-0.6162-1.95160.14391.5801-0.00970.81530.2584-0.04842.25790.44381.460128.8072-15.5881-5.3259
82.01250.03440.09460.15640.3122.02790.2810.0416-0.9602-0.1929-0.47991.12580.8641-0.9254-0.20970.8959-0.4924-0.52190.7587-0.13361.9879-17.6069-21.6806-7.5418
93.92-0.98670.67246.29025.56465.94710.79750.6429-1.3579-0.80920.24920.59161.61110.5742-0.89291.20610.1939-0.67960.7582-0.21371.84332.1965-30.17452.5252
109.5513-3.44535.53152.1418-1.56934.02690.1110.3227-0.3824-0.3555-0.19750.42560.537-0.08790.05020.7957-0.1603-0.21630.7943-0.08461.3181-10.3312-15.3768-6.2413
117.28831.1261-0.6332.27092.04072.9070.3126-0.0198-1.0443-0.42470.08931.98511.0757-1.9737-0.5281.0266-0.4914-0.25761.59210.11222.0284-28.8159-13.5294-9.8693
125.20710.81142.18380.12660.4816.34321.3763-0.066-1.31990.0443-0.32131.56352.3274-0.8689-0.92231.3966-0.4187-0.5491.04960.21652.2548-18.9964-29.7779-2.8289
139.2177-2.44795.91263.243-1.49514.2181.55350.8935-1.7262-0.607-0.41691.91732.07680.5633-1.14041.4567-0.0126-0.49760.9169-0.41631.5903-12.2329-25.2749-16.6425
147.6506-4.77385.02484.57-5.77997.72520.29751.1116-0.387-0.5793-0.85151.34680.5486-0.19560.33271.2676-0.1475-0.55741.1107-0.40041.2841-9.056-17.531-18.7799
152.7841-0.141.98432.84952.24223.34411.45072.4914-2.2716-2.7071-1.14643.53282.91240.2353-0.26052.06930.2537-0.31471.5706-0.18131.88370.5097-32.0532-17.975
163.0471-1.2461-0.24645.28351.55311.6122-0.3047-0.8177-0.80810.86310.1399-0.17181.2040.97720.10771.22350.1028-0.24011.4420.4870.843814.7396-19.820720.506
171.4265-1.948-1.26155.45786.2069.3109-0.45390.6342-0.2417-0.8954-0.36420.3339-1.52290.76150.65111.1723-0.1371-0.21621.0630.31570.774810.7188-13.44816.0972
183.386-3.51951.11054.87910.67452.9844-0.9635-0.4505-0.38962.23950.66740.40991.60120.64570.05751.69320.0531-0.13031.22320.39581.042320.0298-20.694625.7222
198.2367-0.9446-4.50354.43852.49438.2237-0.3304-1.1668-1.19990.79650.72430.75140.6545-0.50610.15091.4707-0.07050.03061.16770.66971.30095.5075-24.565324.1956
205.9753-1.0291-2.17094.76154.72365.5413-0.1421-0.3885-1.24541.35110.35130.48240.1196-0.13920.11221.58640.0783-0.05690.90030.58291.02340.3677-21.713719.1915
213.432-2.2917-0.80762.027-0.88294.4310.37491.967-0.2016-1.3736-0.0884-0.16261.75861.7709-0.32141.4440.4009-0.14512.1825-0.02090.64211.6239-10.5639-31.0445
223.58073.0264-1.78754.57891.59575.67150.01842.06562.6148-1.6691-0.41710.4689-1.01831.44230.11461.5635-0.3272-0.15442.19650.92081.567921.737712.6245-27.358
235.91111.4674-0.84048.2227-2.08838.2770.26141.70770.2495-0.0537-0.4782-0.0774-0.04111.38380.14511.09110.2444-0.10131.68380.1210.71779.7135-7.5434-23.1529
243.87432.0868-3.10085.8279-2.88143.22690.02442.17610.4986-2.2307-0.3507-0.29280.05180.13610.2841.87420.46090.08462.62910.3560.953420.9576-7.907-34.7706
252.5438-0.4201-3.20464.8335-1.52575.01950.34531.74360.0989-1.7594-0.67890.24220.43221.16160.20191.60660.2267-0.32632.29090.28690.68573.0694-1.919-33.7811
261.64690.15451.21983.33420.17111.97850.05580.9734-0.02180.16430.0448-1.0966-0.22340.50781.00711.4478-1.0008-0.87832.30861.11281.706329.829722.4134-6.7111
270.3363-0.32530.28260.4678-0.22260.7924-0.02440.33410.5180.0791-0.1136-0.2049-0.19710.15240.07331.2575-0.8084-1.00882.09031.44081.385423.944516.1365-4.4811
280.2316-0.4854-0.01071.35940.30830.14620.17560.18880.44580.1282-0.3774-1.5644-0.5440.83940.40911.5604-1.0919-0.68582.05521.11652.313933.748528.01-3.591
291.05970.9003-0.511.0263-0.46831.27260.29970.12320.2470.0920.084-0.26990.07210.1862.3741.1657-0.6719-0.60323.16392.60071.369634.74611.864-10.3614
305.3536-0.7502-5.38320.10470.75395.4132-0.22072.63661.1963-1.0850.68710.4720.0731-2.2505-0.49771.3464-0.39880.27863.36781.09661.833832.502913.1655-25.4444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 157 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 39 )
5X-RAY DIFFRACTION5chain 'B' and (resid 40 through 67 )
6X-RAY DIFFRACTION6chain 'B' and (resid 68 through 124 )
7X-RAY DIFFRACTION7chain 'B' and (resid 125 through 157 )
8X-RAY DIFFRACTION8chain 'C' and (resid 9 through 34 )
9X-RAY DIFFRACTION9chain 'C' and (resid 35 through 39 )
10X-RAY DIFFRACTION10chain 'C' and (resid 40 through 67 )
11X-RAY DIFFRACTION11chain 'C' and (resid 68 through 75 )
12X-RAY DIFFRACTION12chain 'C' and (resid 76 through 95 )
13X-RAY DIFFRACTION13chain 'C' and (resid 96 through 123 )
14X-RAY DIFFRACTION14chain 'C' and (resid 124 through 150 )
15X-RAY DIFFRACTION15chain 'C' and (resid 151 through 157 )
16X-RAY DIFFRACTION16chain 'D' and (resid 8 through 39 )
17X-RAY DIFFRACTION17chain 'D' and (resid 40 through 67 )
18X-RAY DIFFRACTION18chain 'D' and (resid 68 through 95 )
19X-RAY DIFFRACTION19chain 'D' and (resid 96 through 124 )
20X-RAY DIFFRACTION20chain 'D' and (resid 125 through 157 )
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 34 )
22X-RAY DIFFRACTION22chain 'E' and (resid 35 through 39 )
23X-RAY DIFFRACTION23chain 'E' and (resid 40 through 75 )
24X-RAY DIFFRACTION24chain 'E' and (resid 76 through 95 )
25X-RAY DIFFRACTION25chain 'E' and (resid 96 through 157 )
26X-RAY DIFFRACTION26chain 'F' and (resid 8 through 39 )
27X-RAY DIFFRACTION27chain 'F' and (resid 40 through 67 )
28X-RAY DIFFRACTION28chain 'F' and (resid 68 through 95 )
29X-RAY DIFFRACTION29chain 'F' and (resid 96 through 150 )
30X-RAY DIFFRACTION30chain 'F' and (resid 151 through 157 )

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