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- PDB-2h34: Apoenzyme crystal structure of the tuberculosis serine/threonine ... -

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Basic information

Entry
Database: PDB / ID: 2h34
TitleApoenzyme crystal structure of the tuberculosis serine/threonine kinase, PknE
ComponentsSerine/threonine-protein kinase pknE
KeywordsTRANSFERASE / apoenzyme / serine/threonine protein kinase
Function / homology
Function and homology information


response to nitrosative stress / negative regulation of fatty acid biosynthetic process / negative regulation of catalytic activity / positive regulation of catalytic activity / : / non-specific serine/threonine protein kinase / protein kinase activity / protein autophosphorylation / protein serine/threonine kinase activity / protein phosphorylation ...response to nitrosative stress / negative regulation of fatty acid biosynthetic process / negative regulation of catalytic activity / positive regulation of catalytic activity / : / non-specific serine/threonine protein kinase / protein kinase activity / protein autophosphorylation / protein serine/threonine kinase activity / protein phosphorylation / integral component of membrane / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Thioredoxin / Thioredoxin-like fold / Thioredoxin-like superfamily / Protein kinase domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Thioredoxin / Thioredoxin-like fold / Thioredoxin-like superfamily / Protein kinase domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Serine/threonine-protein kinase PknE / Serine/threonine-protein kinase PknE
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsGay, L.M. / Ng, H.L. / Alber, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A Conserved Dimer and Global Conformational Changes in the Structure of apo-PknE Ser/Thr Protein Kinase from Mycobacterium tuberculosis.
Authors: Gay, L.M. / Ng, H.L. / Alber, T.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pknE
B: Serine/threonine-protein kinase pknE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2425
Polymers68,1162
Non-polymers1263
Water0
1
A: Serine/threonine-protein kinase pknE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1613
Polymers34,0581
Non-polymers1032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase pknE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0812
Polymers34,0581
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)77.078, 77.078, 221.024
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A & B)

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Components

#1: Protein Serine/threonine-protein kinase pknE


Mass: 34058.152 Da / Num. of mol.: 2 / Fragment: phosphotransfer catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: pknE / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P72001, UniProt: P9WI77*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 2.781035 Å3/Da / Density % sol: 55.771862 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7
Details: 12% PEG 8000, 0.2M NaBr, 0.1M HEPES pH 7.0, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 12.3 / Number: 106124 / Rmerge(I) obs: 0.088 / Χ2: 2.82 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 18268 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.210.07413.285.6
4.796.0310010.074.6785.8
4.184.7910010.0612.6415.9
3.84.1810010.0711.8785.8
3.533.810010.091.4865.8
3.323.5310010.1331.1075.8
3.153.3210010.1970.9545.8
3.023.1510010.2890.8165.8
2.93.0210010.4080.7955.8
2.82.910010.6150.7555.8
ReflectionResolution: 2.8→50 Å / Num. obs: 18268 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.088 / Χ2: 2.816 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.95.80.61518190.7551100
2.9-3.025.80.40818070.7951100
3.02-3.155.80.28918300.8161100
3.15-3.325.80.19718190.9541100
3.32-3.535.80.13318271.1071100
3.53-3.85.80.0918271.4861100
3.8-4.185.80.07118221.8781100
4.18-4.795.90.06118382.6411100
4.79-6.035.80.0718304.6781100
6.03-505.60.074184913.28199.2

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.8 Å / D res low: 50 Å / FOM : 0.34 / Reflection: 17500
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.5590.020.1661.43
2Se600.4280.6590.0361.329
3Se600.9180.3760.1661.465
4Se600.0270.6620.1411.309
5Se600.5930.3850.0541.151
6Se600.3110.2360.0831.168
7Se600.2250.9690.0491.182
8Se600.4040.5540.0410.969
9Se600.2060.8090.0750.71
10Se600.4020.6970.0271.048
11Se600.390.7870.0340.842
12Se600.1470.8040.0870.839
13Se600.1620.8420.0730.782
14Se600.2160.2740.0960.497
15Se600.2080.340.0810.593
16Se600.170.2820.1030.479
Phasing MAD shell
Resolution (Å)FOM Reflection
10.1-500.52830
6.37-10.10.571481
4.98-6.370.491907
4.22-4.980.442251
3.73-4.220.372523
3.37-3.730.292746
3.1-3.370.222872
2.89-3.10.142890
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.64 / Reflection: 17501 / Reflection acentric: 17178 / Reflection centric: 323
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-34.1490.970.970.9578774740
5-80.910.910.782423235766
4-50.860.860.73043298261
3.5-40.750.750.673012296547
3-3.50.450.450.475251518071
2.8-30.230.230.272985294738

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.8→34.1 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.217 / SU B: 34.573 / SU ML: 0.309 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.824 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 908 5.2 %RANDOM
Rwork0.216 ---
all0.218 ---
obs0.218 17499 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 3 0 3645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223707
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9765042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1045478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20422.956159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59915560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8081533
X-RAY DIFFRACTIONr_chiral_restr0.0760.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022857
X-RAY DIFFRACTIONr_nbd_refined0.2350.21751
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.221
X-RAY DIFFRACTIONr_mcbond_it0.4881.52410
X-RAY DIFFRACTIONr_mcangle_it0.94923844
X-RAY DIFFRACTIONr_scbond_it1.7331319
X-RAY DIFFRACTIONr_scangle_it2.7224.51198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.8730.314620.28710811143
2.873-2.9510.319720.26210711143
2.951-3.0360.276630.23511091172
3.036-3.1290.292650.24910781143
3.129-3.2310.306600.23710891149
3.231-3.3430.29670.22710631130
3.343-3.4680.297560.2289921048
3.468-3.6080.211560.18710191075
3.608-3.7660.221550.2129501005
3.766-3.9480.322470.216935982
3.948-4.1580.257440.199899943
4.158-4.4070.248420.206825867
4.407-4.7050.309350.186809844
4.705-5.0740.27330.2756789
5.074-5.5460.222380.224678716
5.546-6.180.245270.259619646
6.18-7.0980.301340.231553587
7.098-8.60.227200.202476496
8.6-11.7930.221210.159358379
11.793-34.10.263110.282231242
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.477-0.4095-0.13164.7689-2.51682.32690.5644-0.98210.54170.9979-0.39031.182-1.0035-0.7901-0.17410.1788-0.0360.2280.3716-0.2320.082111.46814.59621.822
23.039-0.22961.247.25060.66014.0933-0.0490.10750.2151-0.2792-0.2975-0.2821-0.6582-0.10860.34650.00040.3302-0.0638-0.35690.0221-0.24820.50331.2343.326
36.8050.9127-0.37435.9631-1.79773.57550.3343-0.6279-1.31490.0393-0.59420.63290.7747-0.58560.26-0.0278-0.08360.05020.03670.05790.029315.498-4.66114.323
45.8935-1.31390.05376.03862.80714.48730.31760.59070.0933-0.15260.0232-0.55050.27520.4411-0.3409-0.13760.30150.0098-0.30060.1033-0.225438.708-2.5091.75
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA14 - 10034 - 120
22AA101 - 276121 - 296
33BB14 - 10034 - 120
44BB101 - 276121 - 296

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