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- PDB-1uvh: X-ray structure of Dps from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 1uvh
TitleX-ray structure of Dps from Mycobacterium smegmatis
ComponentsSTARVATION-INDUCED DNA PROTECTING PROTEIN
KeywordsDNA BINDING PROTEIN / DNA PROTECTION FROM OXIDATIVE DAMAGE
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm
Similarity search - Function
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 / DNA protection during starvation protein
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIlari, A. / Ceci, P. / Falvo, E. / Chiancone, E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Reassessment of Protein Stability, DNA Binding, and Protection of Mycobacterium Smegmatis Dps.
Authors: Ceci, P. / Ilari, A. / Falvo, E. / Giangiacomo, L. / Chiancone, E.
History
DepositionJan 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: 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.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 / _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: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4198
Polymers81,1954
Non-polymers2234
Water82946
1
A: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules

A: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules

A: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,25624
Polymers243,58612
Non-polymers67012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.300, 124.300, 304.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.00051, 0.57675, -0.81692), (0.57746, -0.66678, -0.4711), (-0.81642, -0.47198, -0.33271)1.33474, 1.66684, 0.66645
2given(0.49915, 0.86652, 7.0E-5), (0.2895, -0.16685, 0.94252), (0.81672, -0.47044, -0.33414)-0.66688, -0.33358, 0.66662
3given(0.50106, -0.28748, -0.81627), (-0.86541, -0.16848, -0.47188), (-0.00187, 0.94285, -0.33321)1.667, 1.33518, 0.3335

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Components

#1: Protein
STARVATION-INDUCED DNA PROTECTING PROTEIN / DPS


Mass: 20298.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VP75, UniProt: P0C558*PLUS
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.5
Details: HEPES 0.1 M, IN A PH RANGE BETWEEN 7.0-7.8. AMMONIUM SULFATE IN A RANGE BETWEEN 1.5-2.0 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorDate: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 22346 / % possible obs: 99 % / Redundancy: 10 % / Rmerge(I) obs: 0.082

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Processing

Software
NameClassification
REFMACrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPS

1dps


Resolution: 2.8→40 Å / Cross valid method: THROUGHOUT
Details: COORDINATES FOR A COMPLETE DODECAMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS ...Details: COORDINATES FOR A COMPLETE DODECAMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS GIVEN BELOW TO THE TETRAMER OF THE ASYMMETRIC UNIT: SYMGEN X,Y,Z SYMGEN Y-X, 1-X,Z SYMGEN 1-Y,1+X-Y,Z
RfactorNum. reflection% reflectionSelection details
Rfree0.34 1117 5 %RANDOM
Rwork0.26 ---
obs0.27 21227 99 %-
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 4 46 4978

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