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- PDB-1rwi: Extracellular domain of Mycobacterium tuberculosis PknD -

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Basic information

Entry
Database: PDB / ID: 1rwi
TitleExtracellular domain of Mycobacterium tuberculosis PknD
ComponentsSerine/threonine-protein kinase pknD
KeywordsTRANSFERASE / beta propeller / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / cellular response to phosphate starvation / positive regulation of catalytic activity / membrane => GO:0016020 / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / non-specific serine/threonine protein kinase ...negative regulation of catalytic activity / negative regulation of fatty acid biosynthetic process / cellular response to phosphate starvation / positive regulation of catalytic activity / membrane => GO:0016020 / protein serine/threonine/tyrosine kinase activity / peptidoglycan-based cell wall / negative regulation of protein binding / manganese ion binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase PknD, NHL repeat domain / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / NHL repeat profile. / NHL repeat / NHL repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase ...Protein kinase PknD, NHL repeat domain / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / NHL repeat profile. / NHL repeat / NHL repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Serine/threonine-protein kinase PknD / Serine/threonine-protein kinase PknD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsGood, M.C. / Greenstein, A.E. / Young, T.A. / Ng, H.L. / Alber, T. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Sensor Domain of the Mycobacterium tuberculosis Receptor Ser/Thr Protein Kinase, PknD, forms a Highly Symmetric beta Propeller.
Authors: Good, M.C. / Greenstein, A.E. / Young, T.A. / Ng, H.L. / Alber, T.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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
B: Serine/threonine-protein kinase pknD
A: Serine/threonine-protein kinase pknD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,61316
Polymers57,0392
Non-polymers1,57414
Water3,675204
1
B: Serine/threonine-protein kinase pknD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,64411
Polymers28,5191
Non-polymers1,12410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase pknD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9695
Polymers28,5191
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.9400, 94.5800, 71.7700
Angle α, β, γ (deg.)90.0000, 98.1000, 90.0000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the monomer

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Components

#1: Protein Serine/threonine-protein kinase pknD


Mass: 28519.459 Da / Num. of mol.: 2 / Fragment: PknD 403-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PKND, RV0931C, MT0958, MTCY08C9.08 / Plasmid: Pet24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon +
References: UniProt: O05871, UniProt: P9WI79*PLUS, EC: 2.7.1.37
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.78 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium acetate, HEPES, cadmium sulfate, p-chloromercurybenzene sulfonic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0781 / Wavelength: 1.0092, 0.9698
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 27, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalMADMx-ray1
2Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07811
21.00921
30.96981
ReflectionResolution: 1.8→15.4 Å / Num. all: 53964 / Num. obs: 53640 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.287 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.052 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
DMmodel building
REFMAC5refinement
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→15.4 Å / Isotropic thermal model: isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22 2529 random
Rwork0.19 --
all0.193 50571 -
obs0.193 49944 -
Displacement parametersBiso mean: 23.835 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 14 204 3992

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