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- PDB-1zth: Crystal Structure of A.fulgidus Rio1 serine protein kinase bound ... -

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Basic information

Entry
Database: PDB / ID: 1zth
TitleCrystal Structure of A.fulgidus Rio1 serine protein kinase bound to ADP and Manganese ion
ComponentsRio1 serine protein kinase
KeywordsTRANSFERASE / protein Kinase / ribosome biogenesis / rRNA / ADP / manganese
Function / homology
Function and homology information


3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity ...3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / hydrolase activity / protein serine kinase activity / ATP binding / metal ion binding
Similarity search - Function
: / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / RIO domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / : / RIO-type serine/threonine-protein kinase Rio1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsWlodawer, A. / LaRonde-LeBlanc, N.
CitationJournal: Febs J. / Year: 2005
Title: Structure and activity of the atypical serine kinase Rio1.
Authors: Laronde-Leblanc, N. / Guszczynski, T. / Copeland, T. / Wlodawer, A.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rio1 serine protein kinase
B: Rio1 serine protein kinase
C: Rio1 serine protein kinase
D: Rio1 serine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,54312
Polymers122,6144
Non-polymers1,9298
Water14,808822
1
A: Rio1 serine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1363
Polymers30,6541
Non-polymers4822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rio1 serine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1363
Polymers30,6541
Non-polymers4822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rio1 serine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1363
Polymers30,6541
Non-polymers4822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rio1 serine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1363
Polymers30,6541
Non-polymers4822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.414, 80.084, 121.056
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rio1 serine protein kinase


Mass: 30653.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: Rio1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS / References: GenBank: 11499392, UniProt: O28471*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 4000, MES, Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9686 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. all: 81701 / Num. obs: 78499 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.147
Reflection shellResolution: 1.89→1.939 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.35 / % possible all: 79.58

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZTF

1ztf


Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.807 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26215 3935 5 %RANDOM
Rwork0.18862 ---
obs0.19224 74564 96.07 %-
all-81701 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.063 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å2-0.48 Å2
2--3.45 Å20 Å2
3----1.75 Å2
Refine analyzeLuzzati coordinate error obs: 0.219 Å
Refinement stepCycle: LAST / Resolution: 1.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7830 0 112 822 8764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228079
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.602210878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31624.274379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.455151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7381550
X-RAY DIFFRACTIONr_chiral_restr0.1260.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025959
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.24234
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.25672
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2751
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.2131
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.262
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3231.54931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.05127700
X-RAY DIFFRACTIONr_scbond_it5.1433607
X-RAY DIFFRACTIONr_scangle_it7.1734.53178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 214 -
Rwork0.197 4518 -
obs--79.58 %

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