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- PDB-2c41: X-ray structure of Dps from Thermosynechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 2c41
TitleX-ray structure of Dps from Thermosynechococcus elongatus
ComponentsDPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
KeywordsIRON-BINDING/OXIDATION PROTEIN / DPS (DNA-BINDING PROTEINS FROM STARVED CELLS) / IRON BINDING / THERMOSTABLE PROTEIN / THERMOPHILIC CYANOBACTERIUM / DNA- BINDING PROTEIN / STRESS PROTEIN / IRON-BINDING-OXIDATION PROTEIN complex
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / DNA binding
Similarity search - Function
Dps protein family signature 2. / 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
TRIETHYLENE GLYCOL / Dps family DNA-binding stress response protein
Similarity search - Component
Biological speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsIlari, A. / Franceschini, S. / Ceci, P. / Chiancone, E.
CitationJournal: FEBS J. / Year: 2006
Title: Antioxidant Dps Protein from the Thermophilic Cyanobacterium Thermosynechococcus Elongatus.
Authors: Franceschini, S. / Ceci, P. / Alaleona, F. / Chiancone, E. / Ilari, A.
History
DepositionOct 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 7, 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 / 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_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
B: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
C: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
D: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
E: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
F: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
G: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
H: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
I: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
J: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
K: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
L: DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,18530
Polymers214,85212
Non-polymers2,33218
Water27,0771503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)122.972, 122.887, 253.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-2046-

HOH

21J-2022-

HOH

31J-2063-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 10 - 158 / Label seq-ID: 10 - 158

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.40193, 0.91516, -0.03054), (0.91501, 0.40015, -0.05128), (-0.0347, -0.04855, -0.99822)16.618, -3.86478, 193.23473
3given(0.83562, -0.19772, -0.51249), (0.36466, -0.49808, 0.78673), (-0.41081, -0.84429, -0.34411)60.32575, -37.65225, 168.29701
4given(-0.49526, 0.71619, 0.49171), (-0.62677, 0.09735, -0.7731), (-0.60156, -0.69108, 0.40067)-23.74801, 122.5386, 98.26976
5given(-0.35966, -0.67048, 0.64893), (-0.16694, 0.73048, 0.66221), (-0.91803, 0.12984, -0.37465)2.13853, -49.14056, 155.40617
6given(-0.49393, -0.6283, -0.60105), (0.7184, 0.09453, -0.68918), (0.48983, -0.7722, 0.40468)124.03357, 72.77737, 66.55423
7given(-0.80848, -0.14629, -0.57005), (-0.14798, -0.88696, 0.4375), (-0.56961, 0.43806, 0.69545)115.19388, 24.3106, 32.31122
8given(0.20641, -0.7696, 0.60424), (-0.76826, -0.5099, -0.38701), (0.60595, -0.38433, -0.6965)-8.041, 109.83905, 155.32558
9given(-0.35577, -0.16961, -0.91906), (-0.66891, 0.73299, 0.12367), (0.65268, 0.65876, -0.37422)135.24895, 17.80989, 89.18413
10given(0.01622, -0.34493, 0.93849), (0.93243, -0.33366, -0.13874), (0.36099, 0.87732, 0.31621)-47.75594, 27.67732, 25.26827
11given(0.01988, 0.93205, 0.36179), (-0.34147, -0.33377, 0.87863), (0.93968, -0.14101, 0.31163)-34.47418, -29.82779, 40.9184
12given(0.83649, 0.3687, -0.40538), (-0.19402, -0.49258, -0.84837), (-0.51248, 0.78831, -0.3405)31.74584, 135.51897, 117.98851

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Components

#1: Protein
DPS FAMILY DNA-BINDING STRESS RESPONSE PROTEIN


Mass: 17904.373 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Strain: BP-1 / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DG54
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1503 / 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: 2.08 Å3/Da / Density % sol: 40.27 %
Crystal growpH: 5
Details: 0.1 M SODIUM ACETATE AT PH VALUES 4.0 AND 5.0, PEG4000 5-15 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 174107 / % possible obs: 97.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.7 % / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JI4

1ji4


Resolution: 1.81→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.212 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 8507 5 %RANDOM
Rwork0.168 ---
obs0.169 161382 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14814 0 150 1503 16467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02215234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.96720596
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.25851841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13425.085708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.257152703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4841560
X-RAY DIFFRACTIONr_chiral_restr0.0780.22359
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211252
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.28821
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.210674
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.21410
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4991.59483
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.713214860
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.46236519
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3074.55736
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: 596 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.030.05
4Dtight positional0.030.05
5Etight positional0.050.05
6Ftight positional0.040.05
7Gtight positional0.030.05
8Htight positional0.040.05
9Itight positional0.030.05
10Jtight positional0.030.05
11Ktight positional0.040.05
12Ltight positional0.050.05
1Amedium positional0.360.5
2Bmedium positional0.390.5
3Cmedium positional0.370.5
4Dmedium positional0.480.5
5Emedium positional0.440.5
6Fmedium positional0.480.5
7Gmedium positional0.370.5
8Hmedium positional0.370.5
9Imedium positional0.30.5
10Jmedium positional0.360.5
11Kmedium positional0.370.5
12Lmedium positional0.350.5
1Atight thermal0.090.5
2Btight thermal0.090.5
3Ctight thermal0.120.5
4Dtight thermal0.080.5
5Etight thermal0.090.5
6Ftight thermal0.090.5
7Gtight thermal0.10.5
8Htight thermal0.10.5
9Itight thermal0.10.5
10Jtight thermal0.150.5
11Ktight thermal0.090.5
12Ltight thermal0.090.5
1Amedium thermal0.532
2Bmedium thermal0.562
3Cmedium thermal0.562
4Dmedium thermal0.542
5Emedium thermal0.582
6Fmedium thermal0.532
7Gmedium thermal0.532
8Hmedium thermal0.572
9Imedium thermal0.592
10Jmedium thermal0.72
11Kmedium thermal0.62
12Lmedium thermal0.552
LS refinement shellResolution: 1.81→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 605
Rwork0.231 11482

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