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- PDB-1o9r: The X-ray crystal structure of Agrobacterium tumefaciens Dps, a m... -

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Basic information

Entry
Database: PDB / ID: 1o9r
TitleThe X-ray crystal structure of Agrobacterium tumefaciens Dps, a member of the family that protect DNA without binding
ComponentsAGROBACTERIUM TUMEFACIENS DPS
KeywordsIRON-BINDING PROTEIN / DNA PROTECTION FROM OXIDATIVE DAMAGE / DNA-BINDING / IRON- 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 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 speciesAGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsIlari, A. / Ceci, P. / Chiancone, E.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The Dps Protein of Agrobacterium Tumefaciens Does not Bind to DNA But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, and Hydroxyl-Radical Scavenging Properties
Authors: Ceci, P. / Ilari, A. / Falvo, E. / Chiancone, E.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structure of the Neutrophil-Activating Protein from Helicobacter Pylori
Authors: Zanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Giudice, G.D. / Rappuoli, R. / Montecucco, C.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Structure of Two Iron-Binding Proteins from Bacillus Anthracis
Authors: Papinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G.
#3: 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.
#4: Journal: Nat.Struct.Biol. / Year: 1998
Title: The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA
Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M.
History
DepositionDec 18, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2003Provider: 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 / _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: AGROBACTERIUM TUMEFACIENS DPS
B: AGROBACTERIUM TUMEFACIENS DPS
C: AGROBACTERIUM TUMEFACIENS DPS
D: AGROBACTERIUM TUMEFACIENS DPS
E: AGROBACTERIUM TUMEFACIENS DPS
F: AGROBACTERIUM TUMEFACIENS DPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,72415
Polymers107,0836
Non-polymers6419
Water13,349741
1
A: AGROBACTERIUM TUMEFACIENS DPS
B: AGROBACTERIUM TUMEFACIENS DPS
C: AGROBACTERIUM TUMEFACIENS DPS
D: AGROBACTERIUM TUMEFACIENS DPS
E: AGROBACTERIUM TUMEFACIENS DPS
F: AGROBACTERIUM TUMEFACIENS DPS
hetero molecules

A: AGROBACTERIUM TUMEFACIENS DPS
B: AGROBACTERIUM TUMEFACIENS DPS
C: AGROBACTERIUM TUMEFACIENS DPS
D: AGROBACTERIUM TUMEFACIENS DPS
E: AGROBACTERIUM TUMEFACIENS DPS
F: AGROBACTERIUM TUMEFACIENS DPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,44830
Polymers214,16512
Non-polymers1,28318
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.046, 90.349, 105.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99802, -0.06293, 0.00092), (-0.06293, 0.99802, 0.00124), (-0.001, 0.00118, -1)108.80263, 3.4124, 52.85859
2given(-0.03312, 0.00097, -0.99945), (0.99892, 0.03275, -0.03307), (0.0327, -0.99946, -0.00205)81.17609, -8.347, 69.90175
3given(-0.03425, -0.00216, 0.99941), (0.99894, 0.03057, 0.0343), (-0.03062, 0.99953, 0.00111)28.50481, -10.10266, -17.10289
4given(-0.03446, 0.99888, 0.03252), (-0.00288, 0.03244, -0.99947), (-0.9994, -0.03454, 0.00176)8.81218, 70.27877, 80.84787
5given(-0.03409, 0.99891, -0.03203), (0.00208, 0.03212, 0.99948), (0.99942, 0.034, -0.00317)10.49781, 17.24392, -27.91645

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Components

#1: Protein
AGROBACTERIUM TUMEFACIENS DPS / DNA-BINDING PROTEIN / DPS-AT


Mass: 17847.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Strain: GV3101 / Plasmid: PET11-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8UCK6
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.26 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5
Details: HEPES 0.1 M, PH 7.0-7.8, ETHYLENE GLYCOL IN A RANGE BETWEEN 16%-24% V/V
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mMTris-HCl1droppH7.5
2200 mM1dropNaCl
37 mg/mlprotein1drop
40.1 MHEPES1reservoirpH7.0-7.8
516-24 %(v/v)ethylene glycol1reservoir

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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: 1.45→50 Å / Num. obs: 179135 / % possible obs: 96 % / Observed criterion σ(I): 0.9 / Redundancy: 5 % / Biso Wilson estimate: 12.44 Å2 / Rmerge(I) obs: 0.053
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 96 %

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Processing

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

1dps


Resolution: 1.45→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2 -5 %RANDOM
Rwork0.17 ---
obs0.18 178396 96 %-
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 0 26 741 8262
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_deg2.4

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