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- PDB-2pzi: Crystal Structure of Protein kinase PknG from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 2pzi
TitleCrystal Structure of Protein kinase PknG from Mycobacterium tuberculosis in Complex with Tetrahydrobenzothiophene AX20017
ComponentsProbable serine/threonine-protein kinase pknG
KeywordsTRANSFERASE / Serine/Threonine-Protein Kinase / ATP-recognition / Kinase-inhibitor complex / Rubredoxin fold / TPR domain
Function / homology
Function and homology information


symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated perturbation of host defenses / glutamine catabolic process / symbiont-mediated suppression of host innate immune response / glutamate catabolic process / evasion of host immune response / : / protein autophosphorylation / non-specific serine/threonine protein kinase / response to antibiotic ...symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated perturbation of host defenses / glutamine catabolic process / symbiont-mediated suppression of host innate immune response / glutamate catabolic process / evasion of host immune response / : / protein autophosphorylation / non-specific serine/threonine protein kinase / response to antibiotic / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein kinase G, rubredoxin domain / Protein kinase G rubredoxin domain / Protein kinase G, tetratricopeptide repeat containing domain / Protein kinase G tetratricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Protein kinase G, rubredoxin domain / Protein kinase G rubredoxin domain / Protein kinase G, tetratricopeptide repeat containing domain / Protein kinase G tetratricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AXX / : / Serine/threonine-protein kinase PknG / Serine/threonine-protein kinase PknG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsHonnappa, S. / Steinmetz, M.O.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for the specific inhibition of protein kinase G, a virulence factor of Mycobacterium tuberculosis.
Authors: Scherr, N. / Honnappa, S. / Kunz, G. / Mueller, P. / Jayachandran, R. / Winkler, F. / Pieters, J. / Steinmetz, M.O.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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

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Assembly

Deposited unit
A: Probable serine/threonine-protein kinase pknG
B: Probable serine/threonine-protein kinase pknG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,70713
Polymers148,3662
Non-polymers1,34211
Water5,332296
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A: Probable serine/threonine-protein kinase pknG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9648
Polymers74,1831
Non-polymers7817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable serine/threonine-protein kinase pknG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7445
Polymers74,1831
Non-polymers5614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.553, 122.553, 243.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable serine/threonine-protein kinase pknG


Mass: 74182.984 Da / Num. of mol.: 2 / Fragment: PknG, Residues 73-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC25618 / Gene: pknG / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P65728, UniProt: P9WI73*PLUS, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 307 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-AXX / 2-[(CYCLOPROPYLCARBONYL)AMINO]-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE


Mass: 264.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O2S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M Sodium Citrate, 0.2M Sodium Chloride, 1M Ammonium phosphate, 0.01M Cadmium Chloride , pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008503 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008503 Å / Relative weight: 1
ReflectionResolution: 2.4→106 Å / Num. all: 80540 / Num. obs: 80540 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.42 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→106 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.871 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.243 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23339 4045 5 %RANDOM
Rwork0.1831 ---
all0.18555 76493 --
obs0.18555 76493 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.621 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9975 0 75 296 10346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210256
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9813956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77151286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65123.052439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.866151624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7661592
X-RAY DIFFRACTIONr_chiral_restr0.090.21609
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027768
X-RAY DIFFRACTIONr_nbd_refined0.2110.24719
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2450
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.29
X-RAY DIFFRACTIONr_mcbond_it2.19126584
X-RAY DIFFRACTIONr_mcangle_it3.482310406
X-RAY DIFFRACTIONr_scbond_it5.7874.54083
X-RAY DIFFRACTIONr_scangle_it7.72663544
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 292 -
Rwork0.25 5629 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7910.6045-0.23271.78660.10621.57940.0258-0.05740.04880.0838-0.01530.07680.0668-0.0751-0.01050.152-0.0440.0310.15290.08090.093719.5399-14.2571-10.1267
20.71861.27691.44688.45474.48915.14140.09820.0167-0.26890.23210.0349-0.64860.28050.3289-0.13310.1499-0.0576-0.03550.16450.04560.116832.8578-18.1186-7.0127
30.58090.3611-0.17782.39680.51190.71270.0638-0.07540.01020.1574-0.06150.15640.0672-0.1206-0.00230.1547-0.0604-0.00190.18380.01040.076329.0197-4.264-6.0253
41.48360.4243-0.142.75061.0832.522-0.01610.18310.0323-0.25860.04380.1252-0.0557-0.1162-0.02770.1688-0.0609-0.01430.20940.05360.121332.24139.1389-14.4526
50.3405-1.4028-0.32886.74142.25221.1550.0771-0.0280.029-0.151-0.04980.3412-0.2547-0.108-0.02730.1308-0.00340.07970.05790.03650.129444.292143.4670.1945
61.51680.1681-0.08261.68240.30013.0350.00020.0695-0.02490.1274-0.0065-0.0152-0.04780.00520.00630.1256-0.03240.02720.11180.03680.159254.679128.8486-4.457
73.2341.93981.20672.75090.06091.6313-0.0060.4159-0.1298-0.28230.1427-0.52670.11360.3235-0.13670.1669-0.00960.06340.1510.04630.140364.067828.0063-11.564
81.2140.0096-0.12891.65570.74221.9206-0.00420.15540.1479-0.0806-0.0280.291-0.1213-0.26430.03220.1310.00850.01210.10070.07010.117139.692232.7768-7.3256
93.9627-1.4422-2.27243.37240.8714.0804-0.2553-0.0182-0.1402-0.1030.05920.86710.1155-0.27130.19610.0570.03290.080.06330.06650.286727.557656.142111.2936
1012.8256-6.5127-6.789310.28824.918312.5551-0.0014-0.43140.6903-0.32620.6289-0.4211-0.63481.2741-0.62750.08-0.06220.00930.2164-0.07620.066740.524369.218410.0532
112.3404-3.35451.56396.5932-1.28621.55620.53220.56090.1506-0.9733-0.8057-0.36830.19910.58460.27350.19030.07760.2380.31410.18990.160298.21540.096911.1534
126.60112.1133-3.765.95951.853810.6881-0.25290.31740.50320.07330.2349-0.2954-0.61640.49030.0180.18170.0689-0.05630.060.00940.0287101.8492-2.169341.2053
134.45830.5564-0.59032.1802-0.60023.5669-0.163-0.0341-0.208-0.0374-0.03950.01210.17330.16870.20260.15310.07050.11360.0630.0660.110994.3978-15.458225.9065
141.0103-0.3170.17393.1093-0.81791.4495-0.01940.0909-0.0467-0.071-0.1438-0.140.13810.18940.16320.16020.05550.05490.18530.09370.142686.4533-3.04721.2648
150.0559-0.45391.15283.6883-9.366923.7885-0.030.52720.63730.7383-0.40640.5841.59590.81750.43640.12490.07790.05440.16490.34170.276284.85914.219534.949
161.94410.2611-0.85662.3984-1.54063.36640.0434-0.18470.130.3515-0.2101-0.2273-0.30750.35970.16660.1803-0.0087-0.04370.12240.07310.147784.989417.488723.9068
171.7825-0.29290.37251.057-0.23631.6666-0.0395-0.13730.15630.22030.00120.0275-0.1622-0.06670.03820.2250.01290.01250.0350.02360.108563.6933.18715.881
180.88041.2206-1.48413.993-3.34683.59340.0833-0.02750.09920.1824-0.3259-0.1746-0.22980.53220.24260.0937-0.06-0.07550.1270.14620.182584.522747.7531-4.342
1921.45123.6185-0.14554.2759-3.46114.85350.5281-0.69860.86630.7844-0.53610.3181-0.76520.02330.0080.141-0.06990.01180.13240.12020.122680.757664.3282-14.2417
201.4024-0.9464-0.4694.3015-4.23145.8038-0.16820.6821-0.3321-0.7743-0.06760.05960.7611-0.33090.23590.1185-0.03780.06040.28160.04950.060174.440275.81477.8415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA69 - 1971 - 128
2X-RAY DIFFRACTION2AA198 - 222129 - 153
3X-RAY DIFFRACTION3AA223 - 298154 - 229
4X-RAY DIFFRACTION4AA299 - 410230 - 341
5X-RAY DIFFRACTION5AA411 - 440342 - 371
6X-RAY DIFFRACTION6AA441 - 473372 - 404
7X-RAY DIFFRACTION7AA474 - 530405 - 461
8X-RAY DIFFRACTION8AA531 - 639462 - 570
9X-RAY DIFFRACTION9AA640 - 714571 - 645
10X-RAY DIFFRACTION10AA715 - 746646 - 677
11X-RAY DIFFRACTION11BB69 - 991 - 31
12X-RAY DIFFRACTION12BB100 - 13532 - 66
13X-RAY DIFFRACTION13BB136 - 19867 - 129
14X-RAY DIFFRACTION14BB199 - 302130 - 233
15X-RAY DIFFRACTION15BB303 - 314234 - 245
16X-RAY DIFFRACTION16BB315 - 408246 - 339
17X-RAY DIFFRACTION17BB409 - 591340 - 522
18X-RAY DIFFRACTION18BB592 - 705523 - 636
19X-RAY DIFFRACTION19BB706 - 729637 - 660
20X-RAY DIFFRACTION20BB730 - 745661 - 676

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