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- PDB-2iy4: X-ray structure of Dps from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 2iy4
TitleX-ray structure of Dps from Listeria monocytogenes
ComponentsNON-HEME IRON-CONTAINING FERRITIN
KeywordsMETAL BINDING PROTEIN / IRON / IRON STORAGE / METAL-BINDING / OXIDATIVE DAMAGE / DPSLM (DNA-BINDING PROTEIN FROM STARVED CELLS) FROM LISTER IRON-INCORPORATION / METAL-BINDING PROTEIN
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 MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsIlari, A. / Bellapadrona, G. / Stefanini, S. / Chiancone, E.
CitationJournal: Proteins / Year: 2007
Title: The Mutations Lys 114 --> Gln and Asp 126 --> Asn Disrupt an Intersubunit Salt Bridge and Convert Listeria Innocua Dps Into its Natural Mutant Listeria Monocytogenes Dps. Effects on Protein Stability at Low Ph.
Authors: Bellapadrona, G. / Chiaraluce, R. / Consalvi, V. / Ilari, A. / Stefanini, S. / Chiancone, E.
History
DepositionJul 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / 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_database_status.status_code_sf / _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.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.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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,98548
Polymers433,64424
Non-polymers1,34024
Water33,1661841
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,43623
Polymers216,82212
Non-polymers61411
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,54825
Polymers216,82212
Non-polymers72613
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.288, 172.708, 135.312
Angle α, β, γ (deg.)90.00, 92.11, 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
12M
22N
32O
42P
52Q
62R
72S
82T
92U
102V
112X
122Y

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A7 - 156
2114B7 - 156
3114C7 - 156
4114D7 - 156
5114E7 - 156
6114F7 - 156
7114G7 - 156
8114H7 - 156
9114I7 - 156
10114J7 - 156
11114K7 - 156
12114L7 - 156
1124M7 - 156
2124N7 - 156
3124O7 - 156
4124P7 - 156
5124Q7 - 156
6124R7 - 156
7124S7 - 156
8124T7 - 156
9124U7 - 156
10124V7 - 156
11124X7 - 156
12124Y7 - 156

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.66987, -0.43939, 0.5985), (-0.42564, -0.43323, -0.79445), (0.60836, -0.78692, 0.10318)87.94193, 44.36348, -16.10238
3given(-0.49658, -0.55196, -0.66988), (-0.54804, -0.3991, 0.7351), (-0.6731, 0.73216, -0.10431)81.62318, 49.67539, 20.45274
4given(0.16587, 0.98404, 0.0645), (0.98382, -0.16962, 0.05773), (0.06774, 0.05388, -0.99625)24.03388, -27.95409, -4.08511
5given(-0.49056, -0.14142, -0.85985), (-0.11075, 0.98886, -0.09945), (0.86434, 0.04645, -0.50076)74.57735, 5.52852, -42.55677
6given(-0.13844, 0.95013, -0.27945), (-0.41409, -0.31185, -0.85515), (-0.89965, -0.00267, 0.43661)39.1878, 41.80017, 43.68299
7given(0.89827, -0.30564, 0.31575), (-0.42255, -0.40336, 0.81164), (-0.12071, -0.86249, -0.49147)9.9426, 43.83567, 20.36374
8given(-0.27109, -0.5026, 0.82092), (0.94977, -0.27822, 0.1433), (0.15637, 0.81853, 0.55277)69.94353, -24.77862, -21.06433
9given(-0.48846, -0.11163, 0.86541), (-0.14353, 0.98855, 0.0465), (-0.8607, -0.1015, -0.4989)73.90559, 7.33132, 43.50167
10given(0.90005, -0.41847, -0.12165), (-0.3068, -0.41022, -0.85883), (0.30949, 0.81031, -0.4976)11.92862, 38.14132, -28.36028
11given(-0.27449, 0.94807, 0.16066), (-0.49535, -0.28262, 0.82143), (0.82418, 0.14589, 0.54721)46.00891, 45.39384, -42.44532
12given(-0.13093, -0.4224, -0.8969), (0.95504, -0.29649, 0.00022), (-0.26601, -0.85655, 0.44223)61.66048, -24.6578, 27.29772
13given(-0.26981, -0.44023, 0.85639), (-0.94524, 0.29072, -0.14835), (-0.18366, -0.84952, -0.49456)24.37774, 24.29491, 89.20048
14given(0.89053, -0.36786, 0.26766), (0.41073, 0.39715, -0.82072), (0.19561, 0.8408, 0.50476)-32.87338, -43.1897, 42.77665
15given(-0.19917, 0.95201, -0.23241), (0.40825, 0.29621, 0.86348), (0.89088, 0.0771, -0.44765)-2.1296, -41.35884, 21.74933
16given(-0.42068, -0.15263, -0.89428), (0.12718, -0.98593, 0.10844), (-0.89825, -0.06812, 0.43418)26.9893, -6.28697, 110.91061
17given(0.92547, -0.34899, -0.14734), (0.29503, 0.42007, 0.85819), (-0.23761, -0.8377, 0.49173)-34.66243, -37.87757, 91.54849
18given(-0.55359, -0.12697, 0.82305), (0.13895, -0.98854, -0.05904), (0.82111, 0.08168, 0.56489)33.11501, -6.91447, 25.1215
19given(-0.1593, -0.47556, -0.86514), (-0.95656, 0.29109, 0.01613), (0.24417, 0.83013, -0.50127)19.80008, 24.68988, 40.84167
20given(-0.20431, 0.95969, 0.19303), (0.51532, 0.2731, -0.81232), (-0.83229, -0.0665, -0.55034)-1.83071, -46.12675, 107.70573
21given(-0.54204, -0.48995, -0.68275), (0.54776, 0.41015, -0.7292), (0.6373, -0.76924, 0.04606)38.59351, -50.07966, 48.04673
22given(0.15254, 0.98821, -0.01284), (-0.98616, 0.15134, -0.06767), (-0.06493, 0.02298, 0.99763)-19.53154, 28.31102, 68.88398
23given(0.99724, -0.01303, 0.07307), (-0.01426, -0.99976, 0.0164), (0.07284, -0.01739, -0.99719)-44.08088, 0.77736, 62.83349
24given(-0.61206, -0.49318, 0.61819), (0.44439, 0.43212, 0.78472), (-0.65415, 0.75501, -0.04532)41.8353, -45.34182, 85.24316

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Components

#1: Protein ...
NON-HEME IRON-CONTAINING FERRITIN / FERRITIN-LIKE PROTEIN / DPS FROM LISTERIA MONOCYTOGENES


Mass: 18068.516 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y8G1
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1841 / 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: 2.38 Å3/Da / Density % sol: 47.91 %
Crystal growpH: 7 / Details: PEG 400 15-30 % W/V, HEPES 0.1 M PH=7.0, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 179045 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 99

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGH

1qgh


Resolution: 2.31→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.413 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 8944 5 %RANDOM
Rwork0.182 ---
obs0.185 169821 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.76 Å2
2--1.56 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.31→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29398 0 24 1841 31263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02230078
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9540582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35553587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.56825.7171569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.318155492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4761572
X-RAY DIFFRACTIONr_chiral_restr0.0930.24412
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.216465
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.220860
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.21890
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7361.518570
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.838228913
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.403312968
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2334.511669
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1218medium positional0.480.5
12B1218medium positional0.420.5
13C1218medium positional0.50.5
14D1218medium positional0.370.5
15E1218medium positional0.470.5
16F1218medium positional0.460.5
17G1218medium positional0.470.5
18H1218medium positional0.450.5
19I1218medium positional0.450.5
110J1218medium positional0.390.5
111K1218medium positional0.580.5
112L1218medium positional0.460.5
21M1211medium positional0.270.5
22N1211medium positional0.380.5
23O1211medium positional0.310.5
24P1211medium positional0.310.5
25Q1211medium positional0.320.5
26R1211medium positional0.310.5
27S1211medium positional0.380.5
28T1211medium positional0.430.5
29U1211medium positional0.420.5
210V1211medium positional0.380.5
211X1211medium positional0.370.5
212Y1211medium positional0.560.5
11A1218medium thermal0.642
12B1218medium thermal0.532
13C1218medium thermal0.62
14D1218medium thermal0.712
15E1218medium thermal0.522
16F1218medium thermal0.62
17G1218medium thermal0.532
18H1218medium thermal0.742
19I1218medium thermal0.532
110J1218medium thermal0.552
111K1218medium thermal0.632
112L1218medium thermal0.512
21M1211medium thermal0.62
22N1211medium thermal0.672
23O1211medium thermal0.522
24P1211medium thermal0.682
25Q1211medium thermal0.522
26R1211medium thermal0.612
27S1211medium thermal0.62
28T1211medium thermal0.512
29U1211medium thermal0.562
210V1211medium thermal0.582
211X1211medium thermal0.512
212Y1211medium thermal0.612
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 595
Rwork0.228 11612

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