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- PDB-3m9g: Crystal structure of the three-PASTA-domain of a Ser/Thr kinase f... -

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Basic information

Entry
Database: PDB / ID: 3m9g
TitleCrystal structure of the three-PASTA-domain of a Ser/Thr kinase from Staphylococcus aureus
ComponentsProtein kinase
KeywordsTRANSFERASE / PASTA DOMAIN / SER/THR KINASE / STK1 / STAPHYLOCOCCUS AUREUS / EXTRACELLULAR DOMAIN / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


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
Similarity search - Function
Serine/threonine protein kinase-like, C-terminal PASTA-like domain / Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Serine/threonine protein kinase-like, C-terminal PASTA-like domain / Trypsin Inhibitor V; Chain A - #20 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Trypsin Inhibitor V; Chain A / 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 / Alpha Beta
Similarity search - Domain/homology
non-specific serine/threonine protein kinase / Non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsParacuellos, P. / Ballandras, A. / Robert, X. / Creze, C. / Cozzone, A.J. / Duclos, B. / Gouet, P.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: The Extended Conformation of the 2.9-A Crystal Structure of the Three-PASTA Domain of a Ser/Thr Kinase from the Human Pathogen Staphylococcus aureus
Authors: Paracuellos, P. / Ballandras, A. / Robert, X. / Kahn, R. / Herve, M. / Mengin-Lecreulx, D. / Cozzone, A.J. / Duclos, B. / Gouet, P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and initial X-ray diffraction study of the three PASTA domains of the Ser/Thr kinase Stk1 from the human pathogen Staphylococcus aureus
Authors: Paracuellos, P. / Ballandras, A. / Robert, X. / Cozzone, A.J. / Duclos, B. / Gouet, P.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8098
Polymers22,3511
Non-polymers4587
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.860, 101.210, 74.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein kinase / / SER/THR KINASE STK1


Mass: 22351.094 Da / Num. of mol.: 1 / Fragment: residues 376-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: SA1063 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q7A5Z8, UniProt: A0A0H3JME9*PLUS, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M IMIDAZOLE pH7.5, 0.8M ZN SULFATE pH 5.23, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-411.282
SYNCHROTRONESRF BM30A21.28253, 1.28314, 1.27557
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 10, 2008
ADSC QUANTUM 315r2CCDNov 10, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SYNCHROTRON MIRRORSSINGLE WAVELENGTHMx-ray1
2SYNCHROTRON MIRRORSMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.282531
31.283141
41.275571
ReflectionResolution: 2.9→20 Å / Num. obs: 8017 / % possible obs: 99.4 % / Redundancy: 6.99 % / Rsym value: 0.091 / Net I/σ(I): 16.71
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 5.08 / Rsym value: 0.433 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→19.77 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.849 / SU B: 18.253 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 0.58 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30457 795 10 %RANDOM
Rwork0.22442 ---
obs0.2327 7151 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: 43.683 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å20 Å2
2---1.76 Å20 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 7 65 1644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221594
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6091.9862142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2885200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6262770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.91615318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.422153
X-RAY DIFFRACTIONr_chiral_restr0.1420.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211170
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 58 -
Rwork0.275 522 -
obs--100 %

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