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

Basic information

• Entry: Database: PDB / ID: 4eqm
• Title: Structural analysis of Staphylococcus aureus serine/threonine kinase PknB
• Components: Protein kinase
• Keywords: TRANSFERASE / Kinase / serine/threonine protein kinase

Function / homology

Function:

protein serine/threonine/tyrosine kinase activity / membrane => GO:0016020 / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / metal ion binding

Domain/homology:

Serine/threonine protein kinase-like, C-terminal PASTA-like domain / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / 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, 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

Component:

PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BENZAMIDINE / non-specific serine/threonine protein kinase / Non-specific serine/threonine protein kinase

• Biological species: Staphylococcus aureus subsp. aureus (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
• Authors: Rakette, S. / Stehle, T.
• Citation: Journal: Plos One / Year: 2012; Title: Structural Analysis of Staphylococcus aureus Serine/Threonine Kinase PknB.; Authors: Rakette, S. / Donat, S. / Ohlsen, K. / Stehle, T.

History

Deposition	Apr 19, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 27, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Protein kinase

B: Protein kinase

C: Protein kinase

D: Protein kinase

E: Protein kinase

F: Protein kinase

hetero molecules

Summary:

• 202 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	202,313	15
Polymers	198,915	6
Non-polymers	3,398	9
Water	0

1

A: Protein kinase

hetero molecules

Summary:

• defined by author&software
• 33.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,779	3
Polymers	33,153	1
Non-polymers	626	2
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

2

B: Protein kinase

hetero molecules

Summary:

• defined by author&software
• 33.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,779	3
Polymers	33,153	1
Non-polymers	626	2
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

3

C: Protein kinase

hetero molecules

Summary:

• defined by author&software
• 33.8 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,779	3
Polymers	33,153	1
Non-polymers	626	2
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

4

D: Protein kinase

hetero molecules

Summary:

• defined by author&software
• 33.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,659	2
Polymers	33,153	1
Non-polymers	506	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

5

E: Protein kinase

hetero molecules

Summary:

• defined by author&software
• 33.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,659	2
Polymers	33,153	1
Non-polymers	506	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

6

F: Protein kinase

hetero molecules

Summary:

• defined by author&software
• 33.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	33,659	2
Polymers	33,153	1
Non-polymers	506	1
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Method	PISA

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 number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
1	2
2	2
3	2
1	3
2	3
3	3
1	4
2	4
3	4
1	5
2	5
3	5
1	6
2	6
3	6
1	7
2	7
3	7
1	8
2	8
3	8
1	9
2	9
3	9
1	10
2	10
3	10
1	11
2	11
3	11
1	12
2	12
3	12
1	13
2	13
3	13
1	14
2	14
3	14
1	15
2	15
3	15
1	16
2	16
3	16
1	17
2	17
3	17
1	18
2	18
3	18

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 7:16 )
2	1	1	chain B and (resseq 7:16 )
3	1	1	chain C and (resseq 7:16 )
1	1	2	chain D and (resseq 7:16 )
2	1	2	chain E and (resseq 7:16 )
3	1	2	chain F and (resseq 7:16 )
1	1	3	chain A and (resseq 22:29 )
2	1	3	chain B and (resseq 22:29 )
3	1	3	chain C and (resseq 22:29 )
1	1	4	chain A and (resseq 35:41 )
2	1	4	chain B and (resseq 35:41 )
3	1	4	chain C and (resseq 35:41 )
1	1	5	chain D and (resseq 22:29 )
2	1	5	chain E and (resseq 22:29 )
3	1	5	chain F and (resseq 22:29 )
1	1	6	chain D and (resseq 35:41 )
2	1	6	chain E and (resseq 35:41 )
3	1	6	chain F and (resseq 35:41 )
1	1	7	chain A and (resseq 51:75 )
2	1	7	chain B and (resseq 51:75 )
3	1	7	chain C and (resseq 51:75 )
1	1	8	chain A and (resseq 83:90 )
2	1	8	chain B and (resseq 83:90 )
3	1	8	chain C and (resseq 83:90 )
1	1	9	chain D and (resseq 51:75 )
2	1	9	chain E and (resseq 51:75 )
3	1	9	chain F and (resseq 51:75 )
1	1	10	chain D and (resseq 83:90 )
2	1	10	chain E and (resseq 83:90 )
3	1	10	chain F and (resseq 83:90 )
1	1	11	chain A and (resseq 97:150)
2	1	11	chain B and (resseq 97:150)
3	1	11	chain C and (resseq 97:150)
1	1	12	chain D and (resseq 97:150)
2	1	12	chain E and (resseq 97:150)
3	1	12	chain F and (resseq 97:150)
1	1	13	chain A and (resseq 174:250)
2	1	13	chain B and (resseq 174:250)
3	1	13	chain C and (resseq 174:250)
1	1	14	chain A and (resseq 259:272)
2	1	14	chain B and (resseq 259:272)
3	1	14	chain C and (resseq 259:272)
1	1	15	chain A and (resseq 273:281)
2	1	15	chain B and (resseq 273:281)
3	1	15	chain C and (resseq 273:281)
1	1	16	chain D and (resseq 174:250)
2	1	16	chain E and (resseq 174:250)
3	1	16	chain F and (resseq 174:250)
1	1	17	chain D and (resseq 259:272)
2	1	17	chain E and (resseq 259:272)
3	1	17	chain F and (resseq 259:272)
1	1	18	chain D and (resseq 273:281)
2	1	18	chain E and (resseq 273:281)
3	1	18	chain 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

Components

#1: Protein

A B C D E F
Protein kinase /

Details:

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 (bacteria)
Strain: N315 / Gene: SA1063 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A5Z8, UniProt: A0A0H3JME9*PLUS

#2: Chemical

A-300 B-300 C-300 D-300 E-300 F-300
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Details:

Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM

#3: Chemical

A-301 B-301 C-301 ChemComp-BEN / BENZAMIDINE / Benzamidine

Details:

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

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.5 ų/Da / Density % sol: 50.72 %
• Crystal grow: Temperature: 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

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
• Detector: Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
• Radiation: Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1 Å / Relative weight: 1
• Reflection: Resolution: 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 shell: Resolution: 3→3.08 Å / % possible all: 99.5

Processing

Software

Name	Version	Classification
RemDAq		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method 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

	Rfactor	Num. reflection	% reflection
Rfree	0.2461	1944	5 %
Rwork	0.2149	-	-
obs	0.2165	38854	99.07 %
all	-	39231	-

• Solvent computation: Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 70.934 Ų / k_sol: 0.315 e/ų

Displacement parameters

	Baniso -1	Baniso -2	Baniso -3
1-	12.9981 Å2	0 Å2	2.2875 Å2
2-	-	8.3536 Å2	-0 Å2
3-	-	-	-13.8873 Å2

Refinement step

Cycle: LAST / Resolution: 3→43.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12420	0	189	0	12609

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	12822
X-RAY DIFFRACTION	f_angle_d	0.918	17444
X-RAY DIFFRACTION	f_dihedral_angle_d	16.257	4822
X-RAY DIFFRACTION	f_chiral_restr	0.078	2043
X-RAY DIFFRACTION	f_plane_restr	0.003	2246

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	85	X-RAY DIFFRACTION	POSITIONAL
1	2	B	85	X-RAY DIFFRACTION	POSITIONAL	0.01
1	3	C	85	X-RAY DIFFRACTION	POSITIONAL	0.027
2	1	D	89	X-RAY DIFFRACTION	POSITIONAL
2	2	E	89	X-RAY DIFFRACTION	POSITIONAL	0.117
2	3	F	89	X-RAY DIFFRACTION	POSITIONAL	0.342
3	1	A	62	X-RAY DIFFRACTION	POSITIONAL
3	2	B	62	X-RAY DIFFRACTION	POSITIONAL	0.005
3	3	C	62	X-RAY DIFFRACTION	POSITIONAL	0.004
4	1	A	51	X-RAY DIFFRACTION	POSITIONAL
4	2	B	51	X-RAY DIFFRACTION	POSITIONAL	0.007
4	3	C	51	X-RAY DIFFRACTION	POSITIONAL	0.006
5	1	D	58	X-RAY DIFFRACTION	POSITIONAL
5	2	E	58	X-RAY DIFFRACTION	POSITIONAL	0.004
5	3	F	58	X-RAY DIFFRACTION	POSITIONAL	0.004
6	1	D	51	X-RAY DIFFRACTION	POSITIONAL
6	2	E	51	X-RAY DIFFRACTION	POSITIONAL	0.005
6	3	F	51	X-RAY DIFFRACTION	POSITIONAL	0.005
7	1	A	203	X-RAY DIFFRACTION	POSITIONAL
7	2	B	203	X-RAY DIFFRACTION	POSITIONAL	0.167
7	3	C	203	X-RAY DIFFRACTION	POSITIONAL	0.004
8	1	A	76	X-RAY DIFFRACTION	POSITIONAL
8	2	B	76	X-RAY DIFFRACTION	POSITIONAL	0.005
8	3	C	76	X-RAY DIFFRACTION	POSITIONAL	0.006
9	1	D	197	X-RAY DIFFRACTION	POSITIONAL
9	2	E	197	X-RAY DIFFRACTION	POSITIONAL	0.008
9	3	F	195	X-RAY DIFFRACTION	POSITIONAL	0.005
10	1	D	76	X-RAY DIFFRACTION	POSITIONAL
10	2	E	76	X-RAY DIFFRACTION	POSITIONAL	0.005
10	3	F	76	X-RAY DIFFRACTION	POSITIONAL	0.005
11	1	A	427	X-RAY DIFFRACTION	POSITIONAL
11	2	B	427	X-RAY DIFFRACTION	POSITIONAL	0.009
11	3	C	427	X-RAY DIFFRACTION	POSITIONAL	0.031
12	1	D	423	X-RAY DIFFRACTION	POSITIONAL
12	2	E	423	X-RAY DIFFRACTION	POSITIONAL	0.073
12	3	F	423	X-RAY DIFFRACTION	POSITIONAL	0.075
13	1	A	585	X-RAY DIFFRACTION	POSITIONAL
13	2	B	585	X-RAY DIFFRACTION	POSITIONAL	0.022
13	3	C	585	X-RAY DIFFRACTION	POSITIONAL	0.021
14	1	A	111	X-RAY DIFFRACTION	POSITIONAL
14	2	B	111	X-RAY DIFFRACTION	POSITIONAL	0.005
14	3	C	111	X-RAY DIFFRACTION	POSITIONAL	0.005
15	1	A	77	X-RAY DIFFRACTION	POSITIONAL
15	2	B	77	X-RAY DIFFRACTION	POSITIONAL	0.004
15	3	C	77	X-RAY DIFFRACTION	POSITIONAL	0.004
16	1	D	571	X-RAY DIFFRACTION	POSITIONAL
16	2	E	571	X-RAY DIFFRACTION	POSITIONAL	0.16
16	3	F	571	X-RAY DIFFRACTION	POSITIONAL	0.011
17	1	D	111	X-RAY DIFFRACTION	POSITIONAL
17	2	E	111	X-RAY DIFFRACTION	POSITIONAL	0.514
17	3	F	111	X-RAY DIFFRACTION	POSITIONAL	0.133
18	1	D	71	X-RAY DIFFRACTION	POSITIONAL
18	2	E	71	X-RAY DIFFRACTION	POSITIONAL	0.005
18	3	F	71	X-RAY DIFFRACTION	POSITIONAL	0.004

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
3-3.075	0.3954	139	0.3406	2636	X-RAY DIFFRACTION	99
3.075-3.1582	0.3751	140	0.3162	2661	X-RAY DIFFRACTION	99
3.1582-3.2511	0.3426	139	0.2965	2632	X-RAY DIFFRACTION	100
3.2511-3.356	0.3515	139	0.2948	2649	X-RAY DIFFRACTION	99
3.356-3.4759	0.3333	137	0.2888	2605	X-RAY DIFFRACTION	100
3.4759-3.615	0.3323	137	0.2932	2603	X-RAY DIFFRACTION	100
3.615-3.7794	0.3087	138	0.2555	2618	X-RAY DIFFRACTION	98
3.7794-3.9785	0.2516	140	0.2305	2664	X-RAY DIFFRACTION	100
3.9785-4.2276	0.2059	138	0.1931	2617	X-RAY DIFFRACTION	99
4.2276-4.5537	0.2287	140	0.1773	2650	X-RAY DIFFRACTION	99
4.5537-5.0114	0.2512	138	0.1884	2631	X-RAY DIFFRACTION	98
5.0114-5.7351	0.2436	138	0.2158	2620	X-RAY DIFFRACTION	99
5.7351-7.2203	0.2432	139	0.2092	2639	X-RAY DIFFRACTION	99
7.2203-43.5174	0.167	142	0.167	2685	X-RAY DIFFRACTION	98