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- PDB-4eqm: Structural analysis of Staphylococcus aureus serine/threonine kin... -

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Basic information

Entry
Database: PDB / ID: 4eqm
TitleStructural analysis of Staphylococcus aureus serine/threonine kinase PknB
ComponentsProtein kinase
KeywordsTRANSFERASE / Kinase / serine/threonine protein kinase
Function / homology
Function and homology information


protein serine/threonine/tyrosine kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / membrane => GO:0016020 / ATP binding / metal ion binding
Similarity search - Function
PASTA / PASTA domain profile. / PASTA domain / PASTA domain / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 ...PASTA / PASTA domain profile. / PASTA domain / PASTA domain / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / 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
Non-specific serine/threonine protein kinase / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BENZAMIDINE / Non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRakette, S. / Stehle, T.
CitationJournal: Plos One / Year: 2012
Title: Structural Analysis of Staphylococcus aureus Serine/Threonine Kinase PknB.
Authors: Rakette, S. / Donat, S. / Ohlsen, K. / Stehle, T.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase
B: Protein kinase
C: Protein kinase
D: Protein kinase
E: Protein kinase
F: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,31315
Polymers198,9156
Non-polymers3,3989
Water0
1
A: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7793
Polymers33,1531
Non-polymers6262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7793
Polymers33,1531
Non-polymers6262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7793
Polymers33,1531
Non-polymers6262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6592
Polymers33,1531
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6592
Polymers33,1531
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6592
Polymers33,1531
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)221.510, 127.550, 70.280
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34
15
25
35
16
26
36
17
27
37
18
28
38
19
29
39
110
210
310
111
211
311
112
212
312
113
213
313
114
214
314
115
215
315
116
216
316
117
217
317
118
218
318

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 7:16 )
211chain B and (resseq 7:16 )
311chain C and (resseq 7:16 )
112chain D and (resseq 7:16 )
212chain E and (resseq 7:16 )
312chain F and (resseq 7:16 )
113chain A and (resseq 22:29 )
213chain B and (resseq 22:29 )
313chain C and (resseq 22:29 )
114chain A and (resseq 35:41 )
214chain B and (resseq 35:41 )
314chain C and (resseq 35:41 )
115chain D and (resseq 22:29 )
215chain E and (resseq 22:29 )
315chain F and (resseq 22:29 )
116chain D and (resseq 35:41 )
216chain E and (resseq 35:41 )
316chain F and (resseq 35:41 )
117chain A and (resseq 51:75 )
217chain B and (resseq 51:75 )
317chain C and (resseq 51:75 )
118chain A and (resseq 83:90 )
218chain B and (resseq 83:90 )
318chain C and (resseq 83:90 )
119chain D and (resseq 51:75 )
219chain E and (resseq 51:75 )
319chain F and (resseq 51:75 )
1110chain D and (resseq 83:90 )
2110chain E and (resseq 83:90 )
3110chain F and (resseq 83:90 )
1111chain A and (resseq 97:150)
2111chain B and (resseq 97:150)
3111chain C and (resseq 97:150)
1112chain D and (resseq 97:150)
2112chain E and (resseq 97:150)
3112chain F and (resseq 97:150)
1113chain A and (resseq 174:250)
2113chain B and (resseq 174:250)
3113chain C and (resseq 174:250)
1114chain A and (resseq 259:272)
2114chain B and (resseq 259:272)
3114chain C and (resseq 259:272)
1115chain A and (resseq 273:281)
2115chain B and (resseq 273:281)
3115chain C and (resseq 273:281)
1116chain D and (resseq 174:250)
2116chain E and (resseq 174:250)
3116chain F and (resseq 174:250)
1117chain D and (resseq 259:272)
2117chain E and (resseq 259:272)
3117chain F and (resseq 259:272)
1118chain D and (resseq 273:281)
2118chain E and (resseq 273:281)
3118chain F and (resseq 273:281)

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
Protein kinase /


Mass: 33152.539 Da / Num. of mol.: 6 / Fragment: UNP residues 1-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (unknown)
Strain: N315 / Gene: SA1063 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A5Z8, UniProt: A0A0H3JME9*PLUS
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2

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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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.06M magnesium chloride, 0.08M MES, 1.3M sodium citrate, 2% benzamidine hydrochloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→43.5 Å / Num. all: 39231 / Num. obs: 38868 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 3→3.08 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→43.5 Å / SU ML: 0.45 / σ(F): 1.99 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 1944 5 %
Rwork0.2149 --
obs0.2165 38854 99.07 %
all-39231 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.934 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.9981 Å20 Å22.2875 Å2
2--8.3536 Å2-0 Å2
3----13.8873 Å2
Refinement stepCycle: LAST / Resolution: 3→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12420 0 189 0 12609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512822
X-RAY DIFFRACTIONf_angle_d0.91817444
X-RAY DIFFRACTIONf_dihedral_angle_d16.2574822
X-RAY DIFFRACTIONf_chiral_restr0.0782043
X-RAY DIFFRACTIONf_plane_restr0.0032246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A85X-RAY DIFFRACTIONPOSITIONAL
12B85X-RAY DIFFRACTIONPOSITIONAL0.01
13C85X-RAY DIFFRACTIONPOSITIONAL0.027
21D89X-RAY DIFFRACTIONPOSITIONAL
22E89X-RAY DIFFRACTIONPOSITIONAL0.117
23F89X-RAY DIFFRACTIONPOSITIONAL0.342
31A62X-RAY DIFFRACTIONPOSITIONAL
32B62X-RAY DIFFRACTIONPOSITIONAL0.005
33C62X-RAY DIFFRACTIONPOSITIONAL0.004
41A51X-RAY DIFFRACTIONPOSITIONAL
42B51X-RAY DIFFRACTIONPOSITIONAL0.007
43C51X-RAY DIFFRACTIONPOSITIONAL0.006
51D58X-RAY DIFFRACTIONPOSITIONAL
52E58X-RAY DIFFRACTIONPOSITIONAL0.004
53F58X-RAY DIFFRACTIONPOSITIONAL0.004
61D51X-RAY DIFFRACTIONPOSITIONAL
62E51X-RAY DIFFRACTIONPOSITIONAL0.005
63F51X-RAY DIFFRACTIONPOSITIONAL0.005
71A203X-RAY DIFFRACTIONPOSITIONAL
72B203X-RAY DIFFRACTIONPOSITIONAL0.167
73C203X-RAY DIFFRACTIONPOSITIONAL0.004
81A76X-RAY DIFFRACTIONPOSITIONAL
82B76X-RAY DIFFRACTIONPOSITIONAL0.005
83C76X-RAY DIFFRACTIONPOSITIONAL0.006
91D197X-RAY DIFFRACTIONPOSITIONAL
92E197X-RAY DIFFRACTIONPOSITIONAL0.008
93F195X-RAY DIFFRACTIONPOSITIONAL0.005
101D76X-RAY DIFFRACTIONPOSITIONAL
102E76X-RAY DIFFRACTIONPOSITIONAL0.005
103F76X-RAY DIFFRACTIONPOSITIONAL0.005
111A427X-RAY DIFFRACTIONPOSITIONAL
112B427X-RAY DIFFRACTIONPOSITIONAL0.009
113C427X-RAY DIFFRACTIONPOSITIONAL0.031
121D423X-RAY DIFFRACTIONPOSITIONAL
122E423X-RAY DIFFRACTIONPOSITIONAL0.073
123F423X-RAY DIFFRACTIONPOSITIONAL0.075
131A585X-RAY DIFFRACTIONPOSITIONAL
132B585X-RAY DIFFRACTIONPOSITIONAL0.022
133C585X-RAY DIFFRACTIONPOSITIONAL0.021
141A111X-RAY DIFFRACTIONPOSITIONAL
142B111X-RAY DIFFRACTIONPOSITIONAL0.005
143C111X-RAY DIFFRACTIONPOSITIONAL0.005
151A77X-RAY DIFFRACTIONPOSITIONAL
152B77X-RAY DIFFRACTIONPOSITIONAL0.004
153C77X-RAY DIFFRACTIONPOSITIONAL0.004
161D571X-RAY DIFFRACTIONPOSITIONAL
162E571X-RAY DIFFRACTIONPOSITIONAL0.16
163F571X-RAY DIFFRACTIONPOSITIONAL0.011
171D111X-RAY DIFFRACTIONPOSITIONAL
172E111X-RAY DIFFRACTIONPOSITIONAL0.514
173F111X-RAY DIFFRACTIONPOSITIONAL0.133
181D71X-RAY DIFFRACTIONPOSITIONAL
182E71X-RAY DIFFRACTIONPOSITIONAL0.005
183F71X-RAY DIFFRACTIONPOSITIONAL0.004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0750.39541390.34062636X-RAY DIFFRACTION99
3.075-3.15820.37511400.31622661X-RAY DIFFRACTION99
3.1582-3.25110.34261390.29652632X-RAY DIFFRACTION100
3.2511-3.3560.35151390.29482649X-RAY DIFFRACTION99
3.356-3.47590.33331370.28882605X-RAY DIFFRACTION100
3.4759-3.6150.33231370.29322603X-RAY DIFFRACTION100
3.615-3.77940.30871380.25552618X-RAY DIFFRACTION98
3.7794-3.97850.25161400.23052664X-RAY DIFFRACTION100
3.9785-4.22760.20591380.19312617X-RAY DIFFRACTION99
4.2276-4.55370.22871400.17732650X-RAY DIFFRACTION99
4.5537-5.01140.25121380.18842631X-RAY DIFFRACTION98
5.0114-5.73510.24361380.21582620X-RAY DIFFRACTION99
5.7351-7.22030.24321390.20922639X-RAY DIFFRACTION99
7.2203-43.51740.1671420.1672685X-RAY DIFFRACTION98

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