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- PDB-3pvp: Structure of Mycobacterium tuberculosis DnaA-DBD in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3pvp
TitleStructure of Mycobacterium tuberculosis DnaA-DBD in complex with box2 DNA
Components
  • Chromosomal replication initiator protein dnaA
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*AP*C)-3')
  • DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / Helical / DNA replication / DNA binding / DnaA-box / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of DNA replication / DNA replication origin binding / DNA replication initiation / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Chromosomal Replication Initiator Protein Dnaa; Chain: A; / DnaA protein, C-terminal DNA-binding domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like ...Chromosomal Replication Initiator Protein Dnaa; Chain: A; / DnaA protein, C-terminal DNA-binding domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / Trp repressor/replication initiator / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTsodikov, O.V. / Biswas, T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA.
Authors: Tsodikov, O.V. / Biswas, T.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromosomal replication initiator protein dnaA
B: Chromosomal replication initiator protein dnaA
C: DNA (5'-D(*CP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*AP*C)-3')
F: DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)39,0336
Polymers39,0336
Non-polymers00
Water1,51384
1
A: Chromosomal replication initiator protein dnaA
C: DNA (5'-D(*CP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)19,5173
Polymers19,5173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-23 kcal/mol
Surface area8890 Å2
MethodPISA
2
B: Chromosomal replication initiator protein dnaA
E: DNA (5'-D(*CP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*AP*C)-3')
F: DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)19,5173
Polymers19,5173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-26 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.677, 88.677, 105.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chromosomal replication initiator protein dnaA


Mass: 11574.367 Da / Num. of mol.: 2 / Fragment: DnaA DBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: dnaA, MRA_0001, Rv0001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5TY69
#2: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*AP*C)-3')


Mass: 3895.563 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*GP*TP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*G)-3')


Mass: 4046.645 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mM Tris, 2 mM MgCl2, 50 mM NaCl, 1200 mM NH4SO4, 2-5% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris11
2MgCl211
3NaCl11
4NH4SO411
5glycerol11
6Tris12
7MgCl212
8NaCl12
9NH4SO412
10glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21973 / % possible obs: 87.1 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23821 1034 5.2 %RANDOM
Rwork0.22094 ---
all0.222 20594 --
obs0.22184 18916 91.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 1054 0 84 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212714
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9242.4493874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.035189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44621.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14215293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2941522
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021670
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
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% reflection
Rfree0.346 44 -
Rwork0.313 919 -
obs--61.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.46410.93420.48711.3791-0.47831.258-0.0770.06640.0307-0.0676-0.0050.03030.03510.07910.0820.4140.00190.01480.43320.01840.1706-34.87924.74422.425
21.90.00240.37751.43140.5671.5124-0.09030.20730.1571-0.1570.02550.0068-0.15550.09830.06490.434-0.0063-0.02690.4380.03010.1753-33.58644.3410.636
30.60940.8831-1.33731.5074-2.36283.7603-0.00910.05550.0227-0.19720.15990.05270.4283-0.2445-0.15090.4222-0.0267-0.0480.41120.02190.1839-52.29218.18117.085
41.4371-0.1217-1.36170.3156-0.53748.1993-0.0360.0098-0.0234-0.06410.10410.07760.2891-0.5842-0.06810.4423-0.0336-0.00630.31750.02650.1619-50.84918.37517.662
50.17220.1142-0.10440.4870.81362.33890.027-0.0311-0.0043-0.14430.04890.0129-0.4786-0.2478-0.0760.57580.0409-0.09710.52350.05190.2038-47.43154.90519.448
62.4581-1.00860.51410.7858-1.24273.0389-0.0457-0.21170.17130.05320.16530.0225-0.0982-0.3191-0.11950.5471-0.007-0.08390.3179-0.01680.2181-46.12354.69918.653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A411 - 506
2X-RAY DIFFRACTION2B411 - 505
3X-RAY DIFFRACTION3C101 - 113
4X-RAY DIFFRACTION4D201 - 213
5X-RAY DIFFRACTION5E101 - 113
6X-RAY DIFFRACTION6F201 - 213

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