[English] 日本語
Yorodumi
- PDB-4psk: Mycobacterium tuberculosis RecA phosphate bound low temperature s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4psk
TitleMycobacterium tuberculosis RecA phosphate bound low temperature structure I-LT
ComponentsProtein RecA, 1st part, 2nd part
KeywordsHYDROLASE / HOMOLOGOUS RECOMBINATION / DNA REPAIR / ATPASE / RECOMBINASE / DNA BINDING PROTEIN / PLOOP CONTAINING NTPASE FOLD / ATP BINDING / HYDROLYSIS
Function / homology
Function and homology information


DNA strand invasion / DNA strand exchange activity / UV protection / intein-mediated protein splicing / intron homing / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...DNA strand invasion / DNA strand exchange activity / UV protection / intein-mediated protein splicing / intron homing / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity / manganese ion binding / single-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / response to antibiotic / DNA repair / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
RecA protein, C-terminal domain / Rec A Protein; domain 2 / LAGLIDADG-like domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : ...RecA protein, C-terminal domain / Rec A Protein; domain 2 / LAGLIDADG-like domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : / recA bacterial DNA recombination protein / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChandran, A.V. / Prabu, J.R. / Patil, N.K. / Muniyappa, K. / Vijayan, M.
Citation
Journal: J.Biosci. / Year: 2015
Title: Structural studies on Mycobacterium tuberculosis RecA: Molecular plasticity and interspecies variability
Authors: Chandran, A.V. / Prabu, J.R. / Nautiyal, A. / Patil, K.N. / Muniyappa, K. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes
Authors: Prabu, J.R. / Manjunath, G.P. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#2: Journal: Nucleic Acids Res. / Year: 2006
Title: Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery
Authors: Krishna, R. / Manjunath, G.P. / Kumar, P. / Surolia, A. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#3: Journal: J.Bacteriol. / Year: 2003
Title: Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes
Authors: Datta, S. / Krishna, R. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#4: Journal: Proteins / Year: 2003
Title: Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition
Authors: Datta, S. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
#5: Journal: Nucleic Acids Res. / Year: 2000
Title: Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation
Authors: Datta, S. / Prabu, M.M. / Vaze, M.B. / Ganesh, N. / Chandra, N.R. / Muniyappa, K. / Vijayan, M.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein RecA, 1st part, 2nd part
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3172
Polymers37,2221
Non-polymers951
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.120, 107.120, 71.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Protein RecA, 1st part, 2nd part / Recombinase A


Mass: 37222.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2806, MTV002.02c, recA, Rv2737c / Plasmid: PEJ135 / Production host: Escherichia coli (E. coli) / Strain (production host): KM4104
References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN IS EXPRESSED AS A 790 AMINO ACID RESIDUE PRECURSOR (UNIPROT P0A5U4). ONCE IT IS ...THE PROTEIN IS EXPRESSED AS A 790 AMINO ACID RESIDUE PRECURSOR (UNIPROT P0A5U4). ONCE IT IS RELEASED INTO THE CELL, THE CHAIN MTU RECA INTEIN (RESIDUES 252-691) IS CLEAVED OFF, CHAINS 1ST PART (RESIDUES 1-251) AND 2ND PART (RESIDUES 692-790) JOIN TOGETHER TO FORM THE MATURE PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 30% PEG 3350, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 2008
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.8→38.87 Å / Num. obs: 11506 / Redundancy: 3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / Num. unique all: 1633

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G19

1g19


Resolution: 2.8→29.61 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.367 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.79 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25414 1147 10 %RANDOM
Rwork0.19222 ---
obs0.19816 10332 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.72 Å20 Å2
2---0.72 Å20 Å2
3---2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 5 51 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192268
X-RAY DIFFRACTIONr_bond_other_d0.0010.022209
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9823062
X-RAY DIFFRACTIONr_angle_other_deg0.69335058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3245305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50124.60789
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6551516
X-RAY DIFFRACTIONr_chiral_restr0.0550.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 72 -
Rwork0.298 727 -
obs--96.27 %

+
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://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