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- PDB-1sd5: Crystal structure of Rv1626 -

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Basic information

Entry
Database: PDB / ID: 1sd5
TitleCrystal structure of Rv1626
Componentsputative antiterminatorAntitermination
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / rv1626 / transcriptional / antiterminator / two components 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
IODIDE ION / Probable transcriptional regulatory protein PdtaR / Transcriptional regulatory protein PdtaR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 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 13, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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

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Assembly

Deposited unit
A: putative antiterminator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,60416
Polymers22,7001
Non-polymers1,90415
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.558, 44.558, 180.965
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 / Antitermination


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-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4
Details: 15 % 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: BW7A / Wavelength: 0.981 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.68→40 Å / Num. all: 22233 / Num. obs: 22233 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 18.16 Å2 / Rsym value: 0.036 / Net I/σ(I): 32.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.834 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21637 1118 5.1 %RANDOM
Rwork0.1708 ---
all0.17429 20732 --
obs0.17302 20724 99.96 %-
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: 11.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.68→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 15 206 1690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221487
X-RAY DIFFRACTIONr_bond_other_d00.021471
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9872006
X-RAY DIFFRACTIONr_angle_other_deg0.62233395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.0155187
X-RAY DIFFRACTIONr_chiral_restr0.0670.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
X-RAY DIFFRACTIONr_nbd_refined0.2360.2355
X-RAY DIFFRACTIONr_nbd_other0.2650.21766
X-RAY DIFFRACTIONr_nbtor_other0.0850.2950
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.219
X-RAY DIFFRACTIONr_mcbond_it1.3771.5941
X-RAY DIFFRACTIONr_mcangle_it2.30721517
X-RAY DIFFRACTIONr_scbond_it3.9393546
X-RAY DIFFRACTIONr_scangle_it6.0914.5489
X-RAY DIFFRACTIONr_sphericity_free13.669219
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 88
Rwork0.21 1475

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