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- PDB-1ys3: Crystal Structure of the ATP binding domain of PrrB from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 1ys3
TitleCrystal Structure of the ATP binding domain of PrrB from Mycobacterium Tuberculosis
ComponentsSensor-type histidine kinase prrB
KeywordsTRANSFERASE / Histidine Kinase / ATP-binding domain / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / Structural Genomics
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / peptidoglycan-based cell wall / protein autophosphorylation / membrane => GO:0016020 / protein kinase activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sensor-type histidine kinase PrrB / Sensor-type histidine kinase PrrB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsNowak, E. / Panjikar, S. / Tucker, P. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: To be Published
Title: Crystal structure of ATP binding domain of Hidtidine Kinase from MTB
Authors: Nowak, E. / Panjikar, S. / Tucker, P.
History
DepositionFeb 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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: Sensor-type histidine kinase prrB
B: Sensor-type histidine kinase prrB
C: Sensor-type histidine kinase prrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1016
Polymers45,7353
Non-polymers3663
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.476, 61.476, 211.333
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Sensor-type histidine kinase prrB / Histidine Kinase


Mass: 15245.019 Da / Num. of mol.: 3 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MTB / Plasmid: PetM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P0A5Z8, UniProt: P9WGK7*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG200DME, Ca acetate, Bis Tris Propane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.111
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.92
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 20, 2004
MARRESEARCH2CCDMay 15, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Double crystal focussing monochromator chromator
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.921
ReflectionResolution: 1.9→20 Å / Num. all: 34641 / Num. obs: 32808 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.27 % / Rsym value: 0.075 / Net I/σ(I): 31.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2 / Num. unique all: 3087 / Rsym value: 0.66 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.583 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23523 1730 5 %RANDOM
Rwork0.18596 ---
all0.18851 34641 --
obs0.18851 32808 97.65 %-
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: 35.732 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 24 206 3198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223031
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9964137
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.44724.202119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75415450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2851524
X-RAY DIFFRACTIONr_chiral_restr0.1380.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21273
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22020
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3780.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4091.52113
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3952.53273
X-RAY DIFFRACTIONr_scbond_it5.28251002
X-RAY DIFFRACTIONr_scangle_it8.45810864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 100 -
Rwork0.246 2108 -
obs--85.95 %

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