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- PDB-1s8n: Crystal structure of Rv1626 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1s8n
TitleCrystal structure of Rv1626 from Mycobacterium tuberculosis
Componentsputative antiterminator
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rv1626 / TRANSCRIPTIONAL ANTITERMINATOR / TWO COMPONENT SYSTEM / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


anion binding / phosphorelay signal transduction system / peptidoglycan-based cell wall / transcription antitermination / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
: / Signal transduction response regulator, antiterminator / ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...: / Signal transduction response regulator, antiterminator / ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Probable transcriptional regulatory protein PdtaR / Transcriptional regulatory protein PdtaR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å
AuthorsMorth, J.P. / Feng, V. / Perry, L.J. / Svergun, D.I. / Tucker, P.A. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Structure / Year: 2004
Title: The Crystal and Solution Structure of a Putative Transcriptional Antiterminator from Mycobacterium tuberculosis.
Authors: Morth, J.P. / Feng, V. / Perry, L.J. / Svergun, D.I. / Tucker, P.A.
History
DepositionFeb 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative antiterminator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7422
Polymers22,7001
Non-polymers421
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.836, 44.836, 180.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein putative antiterminator


Mass: 22700.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: phosphorylation dependent transcriptional antitermination regulator
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rv1626 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP / References: UniProt: O06143, UniProt: P9WGM3*PLUS
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4
Details: PEG 1.5K, pure water, pH 4, Micro batch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 1.482→45 Å / Num. obs: 29935 / Redundancy: 6.2 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.037 / Net I/σ(I): 21.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sd5

1sd5


Resolution: 1.482→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.569 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22835 1570 5 %RANDOM
Rwork0.2029 ---
all0.2042 30649 --
obs0.2042 29676 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.467 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.482→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 3 201 1685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221537
X-RAY DIFFRACTIONr_bond_other_d00.021546
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9862071
X-RAY DIFFRACTIONr_angle_other_deg0.65933565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.2045189
X-RAY DIFFRACTIONr_chiral_restr0.0840.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021653
X-RAY DIFFRACTIONr_gen_planes_other00.02303
X-RAY DIFFRACTIONr_nbd_refined0.2460.2350
X-RAY DIFFRACTIONr_nbd_other0.2660.21828
X-RAY DIFFRACTIONr_nbtor_other0.0850.2979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3560.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.219
X-RAY DIFFRACTIONr_mcbond_it1.7081.5956
X-RAY DIFFRACTIONr_mcangle_it2.69221553
X-RAY DIFFRACTIONr_scbond_it3.9053581
X-RAY DIFFRACTIONr_scangle_it5.954.5518
LS refinement shellResolution: 1.482→1.521 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 112
Rwork0.267 1814

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