[English] 日本語
Yorodumi
- PDB-3pvp: Structure of Mycobacterium tuberculosis DnaA-DBD in complex with ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more