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- PDB-2bkc: The X-ray structure of the H43G Listeria innocua Dps mutant -

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Basic information

Entry
Database: PDB / ID: 2bkc
TitleThe X-ray structure of the H43G Listeria innocua Dps mutant
ComponentsNON-HEME IRON-CONTAINING FERRITIN
KeywordsIRON OXIDATION AND STORAGE / DPS (DNA BINDING PROTEIN FROM STARVED CELLS) / DPS FERROXIDASE CENTER / MUTAGENESIS STUDY / IRON STORAGE / METAL TRANSPORT / IRON OXIDATION
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: 2.3 Å
AuthorsIlari, A. / Stefanini, S. / Chiancone, E.
Citation
Journal: Biochemistry / Year: 2005
Title: The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants.
Authors: Ilari, A. / Latella, M.C. / Ceci, P. / Ribacchi, F. / Su, M. / Giangiacomo, L. / Stefanini, S. / Chasteen, N.D. / Chiancone, E.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The Dodecameric Ferritin from Listeria Innocua Contains a Novel Intersubunit Iron-Binding Site
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
History
DepositionFeb 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NON-HEME IRON-CONTAINING FERRITIN
B: NON-HEME IRON-CONTAINING FERRITIN
C: NON-HEME IRON-CONTAINING FERRITIN
D: NON-HEME IRON-CONTAINING FERRITIN
E: NON-HEME IRON-CONTAINING FERRITIN
F: NON-HEME IRON-CONTAINING FERRITIN
G: NON-HEME IRON-CONTAINING FERRITIN
H: NON-HEME IRON-CONTAINING FERRITIN
I: NON-HEME IRON-CONTAINING FERRITIN
J: NON-HEME IRON-CONTAINING FERRITIN
K: NON-HEME IRON-CONTAINING FERRITIN
L: NON-HEME IRON-CONTAINING FERRITIN
M: NON-HEME IRON-CONTAINING FERRITIN
N: NON-HEME IRON-CONTAINING FERRITIN
O: NON-HEME IRON-CONTAINING FERRITIN
P: NON-HEME IRON-CONTAINING FERRITIN
Q: NON-HEME IRON-CONTAINING FERRITIN
R: NON-HEME IRON-CONTAINING FERRITIN
S: NON-HEME IRON-CONTAINING FERRITIN
T: NON-HEME IRON-CONTAINING FERRITIN
U: NON-HEME IRON-CONTAINING FERRITIN
V: NON-HEME IRON-CONTAINING FERRITIN
X: NON-HEME IRON-CONTAINING FERRITIN
Y: NON-HEME IRON-CONTAINING FERRITIN


Theoretical massNumber of molelcules
Total (without water)431,74724
Polymers431,74724
Non-polymers00
Water3,279182
1
A: NON-HEME IRON-CONTAINING FERRITIN
B: NON-HEME IRON-CONTAINING FERRITIN
C: NON-HEME IRON-CONTAINING FERRITIN
D: NON-HEME IRON-CONTAINING FERRITIN
E: NON-HEME IRON-CONTAINING FERRITIN
F: NON-HEME IRON-CONTAINING FERRITIN
G: NON-HEME IRON-CONTAINING FERRITIN
H: NON-HEME IRON-CONTAINING FERRITIN
I: NON-HEME IRON-CONTAINING FERRITIN
J: NON-HEME IRON-CONTAINING FERRITIN
K: NON-HEME IRON-CONTAINING FERRITIN
L: NON-HEME IRON-CONTAINING FERRITIN


Theoretical massNumber of molelcules
Total (without water)215,87412
Polymers215,87412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
M: NON-HEME IRON-CONTAINING FERRITIN
N: NON-HEME IRON-CONTAINING FERRITIN
O: NON-HEME IRON-CONTAINING FERRITIN
P: NON-HEME IRON-CONTAINING FERRITIN
Q: NON-HEME IRON-CONTAINING FERRITIN
R: NON-HEME IRON-CONTAINING FERRITIN
S: NON-HEME IRON-CONTAINING FERRITIN
T: NON-HEME IRON-CONTAINING FERRITIN
U: NON-HEME IRON-CONTAINING FERRITIN
V: NON-HEME IRON-CONTAINING FERRITIN
X: NON-HEME IRON-CONTAINING FERRITIN
Y: NON-HEME IRON-CONTAINING FERRITIN


Theoretical massNumber of molelcules
Total (without water)215,87412
Polymers215,87412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.726, 175.648, 135.957
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231X
241Y

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A7 - 156
2115B7 - 156
3115C7 - 156
4115D7 - 156
5115E7 - 156
6115F7 - 156
7115G7 - 156
8115H7 - 156
9115I7 - 156
10115J7 - 156
11115K7 - 156
12115L7 - 156
13115M7 - 156
14115N7 - 156
15115O7 - 156
16115P7 - 156
17115Q7 - 156
18115R7 - 156
19115S7 - 156
20115T7 - 156
21115U7 - 156
22115V7 - 156
23115X7 - 156
24115Y7 - 156

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.50803, -0.5498, -0.66304), (-0.53996, -0.39646, 0.74247), (-0.67108, 0.73521, -0.09546)6.25322, 2.01804, 2.64179
3given(0.17894, 0.98185, 0.06278), (0.98071, -0.18311, 0.06839), (0.07864, 0.04933, -0.99568)3.10761, -3.61549, 0.27097
4given(-0.67267, -0.42797, 0.60362), (-0.44592, -0.41653, -0.79225), (0.59048, -0.80209, 0.08935)6.82983, 1.7457, -2.29695
5given(0.89109, -0.31984, 0.32196), (-0.43273, -0.38504, 0.81516), (-0.13675, -0.8657, -0.48151)0.35085, 1.75017, 0.84402
6given(-0.49211, -0.13421, -0.86013), (-0.10826, 0.98981, -0.09251), (0.86378, 0.04759, -0.50162)6.24416, 0.24706, -3.24329
7given(-0.13152, 0.94902, -0.28647), (-0.41024, -0.31518, -0.85579), (-0.90245, 0.00497, 0.43077)4.29444, 1.73351, 3.76426
8given(-0.2837, -0.50384, 0.81588), (0.94358, -0.29822, 0.14394), (0.17079, 0.81069, 0.56001)4.81433, -3.81265, -0.89155
9given(0.88979, -0.43705, -0.13137), (-0.32459, -0.4037, -0.85538), (0.32081, 0.80375, -0.50107)0.4396, 1.42719, -0.99248
10given(-0.12999, -0.41648, -0.8998), (0.95236, -0.30496, 0.00357), (-0.27589, -0.85647, 0.43628)4.88246, -3.75199, 1.05231
11given(-0.26399, 0.95071, 0.16268), (-0.51063, -0.28084, 0.81264), (0.81827, 0.13146, 0.5596)5.23317, 1.93746, -3.0838
12given(-0.49455, -0.09618, 0.86381), (-0.11523, 0.99234, 0.04453), (-0.86148, -0.07751, -0.50185)5.70967, 0.55058, 3.72477
13given(0.4093, 0.15139, 0.89975), (0.13022, -0.98574, 0.10662), (0.90306, 0.07353, -0.42317)33.48466, 53.4533, 66.17545
14given(-0.88859, 0.38111, -0.25527), (0.4048, 0.3898, -0.82716), (-0.21574, -0.83834, -0.50065)38.90019, 52.04409, 70.4029
15given(0.28696, 0.42763, -0.8572), (-0.93463, 0.32118, -0.15265), (0.21003, 0.84497, 0.49184)34.64077, 57.6897, 68.50392
16given(0.1996, -0.95402, 0.2236), (0.40589, 0.2882, 0.86729), (-0.89186, -0.08236, 0.44476)34.79517, 51.98711, 72.89703
17given(0.19364, -0.96163, -0.19437), (0.52316, 0.26881, -0.80873), (0.82994, 0.05491, 0.55514)35.14251, 51.93525, 66.05379
18given(0.56292, 0.12585, -0.81687), (0.12228, -0.99014, -0.06828), (-0.81742, -0.06145, -0.57276)33.34949, 53.34518, 72.70346
19given(-0.92138, 0.35691, 0.15384), (0.30572, 0.42119, 0.85389), (0.23997, 0.8338, -0.49719)39.24445, 52.47857, 68.46288
20given(0.1795, 0.48247, 0.85732), (-0.95085, 0.30861, 0.02541), (-0.25232, -0.81975, 0.51415)34.47528, 57.66699, 70.17834
21given(0.60628, 0.48608, -0.6294), (0.45994, 0.43133, 0.77615), (0.64875, -0.76005, 0.03793)32.93309, 51.78677, 67.06021
22given(-0.17045, -0.98502, 0.02611), (-0.98315, 0.16823, -0.07154), (0.06608, -0.03786, -0.9971)35.96334, 57.73688, 69.18856
23given(0.5525, 0.47307, 0.68625), (0.54725, 0.41512, -0.72677), (-0.62869, 0.77709, -0.02954)33.09411, 51.65105, 71.72962
24given(-0.99519, 0.02772, -0.09399), (-0.02945, -0.99942, 0.0171), (-0.09346, 0.01979, 0.99543)39.38564, 53.88029, 69.34566

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Components

#1: Protein ...
NON-HEME IRON-CONTAINING FERRITIN / FERRITIN-LIKE PROTEIN


Mass: 17989.459 Da / Num. of mol.: 24 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: H43G LISTERIA INNOCUA DPS MUTANT / Source: (gene. exp.) LISTERIA INNOCUA (bacteria) / Plasmid: PET-11A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P80725
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: PARTICIPATE IN IRON STORAGE ENGINEERED MUTATION IN CHAIN A, B, C, D, E, F, G, H, I, J, K, ...FUNCTION: PARTICIPATE IN IRON STORAGE ENGINEERED MUTATION IN CHAIN A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, X, Y HIS 43 TO GLY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 40.9 %
Crystal growDetails: PEG 100 15-30% W/V, ACETATE BUFFERS AT PH VALUES BETWEEN 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 172339 / % possible obs: 91.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGH

1qgh


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 8690 5.1 %RANDOM
Rwork0.209 ---
obs0.212 163334 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å2-0.55 Å2
2--0.3 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29174 0 0 182 29356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02129822
X-RAY DIFFRACTIONr_bond_other_d0.0020.0226423
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.95440199
X-RAY DIFFRACTIONr_angle_other_deg0.908361924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88853575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.24372
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0232897
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025831
X-RAY DIFFRACTIONr_nbd_refined0.2140.26950
X-RAY DIFFRACTIONr_nbd_other0.2330.228060
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.216210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6391.517857
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.255228737
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.216311965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6674.511462
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
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 645
Rwork0.241 11638

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