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- PDB-5xlm: Monomer form of M.tuberculosis PknI sensor domain -

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Basic information

Entry
Database: PDB / ID: 5xlm
TitleMonomer form of M.tuberculosis PknI sensor domain
ComponentsSerine/threonine-protein kinase PknI
KeywordsTRANSFERASE / monomer / sensor domain / PknI / M.tuberculosis
Function / homology
Function and homology information


regulation of growth rate / manganese ion binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase PknI
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRao, Z. / Yan, Q.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology2014CB542800 China
National Natural Science Foundation of China (NSFC)81330036 China
National Natural Science Foundation of China (NSFC)81520108019 China
CitationJournal: Structure / Year: 2017
Title: Structural Insight into the Activation of PknI Kinase from M. tuberculosis via Dimerization of the Extracellular Sensor Domain.
Authors: Yan, Q. / Jiang, D. / Qian, L. / Zhang, Q. / Zhang, W. / Zhou, W. / Mi, K. / Guddat, L. / Yang, H. / Rao, Z.
History
DepositionMay 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknI
B: Serine/threonine-protein kinase PknI


Theoretical massNumber of molelcules
Total (without water)45,2602
Polymers45,2602
Non-polymers00
Water1,47782
1
A: Serine/threonine-protein kinase PknI


Theoretical massNumber of molelcules
Total (without water)22,6301
Polymers22,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PknI


Theoretical massNumber of molelcules
Total (without water)22,6301
Polymers22,6301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.791, 58.791, 92.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Serine/threonine-protein kinase PknI


Mass: 22630.197 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 402-585
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pknI, Rv2914c, MTCY338.02c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WI69, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M succinic acid, pH 7.0, 0.1M HEPES, 1% w/v PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97906 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18077 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.028 / Net I/σ(I): 28.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 909 / Rpim(I) all: 0.028 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.558 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.26
RfactorNum. reflection% reflection
Rfree0.2559 734 4.28 %
Rwork0.2203 --
obs0.222 17140 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 0 82 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032293
X-RAY DIFFRACTIONf_angle_d0.6583154
X-RAY DIFFRACTIONf_dihedral_angle_d16.539856
X-RAY DIFFRACTIONf_chiral_restr0.046361
X-RAY DIFFRACTIONf_plane_restr0.005418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.37020.32211410.25392590X-RAY DIFFRACTION75
2.3702-2.60870.3241990.2633498X-RAY DIFFRACTION100
2.6087-2.98610.26641860.24643433X-RAY DIFFRACTION100
2.9861-3.76190.23661670.22283441X-RAY DIFFRACTION100
3.7619-44.56740.23431410.19033444X-RAY DIFFRACTION99

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