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- PDB-1zp9: Crystal Structure of full-legnth A.fulgidus Rio1 Serine Kinase bo... -

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Basic information

Entry
Database: PDB / ID: 1zp9
TitleCrystal Structure of full-legnth A.fulgidus Rio1 Serine Kinase bound to ATP and Mn2+ ions.
ComponentsRio1 kinase
KeywordsTRANSFERASE / Rio1 / RioK1 / serine kinase / protein kinase / Manganese / Ribosome biogenesis
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / hydrolase activity / protein serine kinase activity / protein serine/threonine 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 / RIO1 family / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / RIO-type serine/threonine-protein kinase Rio1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWlodawer, A. / LaRonde-LeBlanc, N.
Citation
Journal: Febs J. / Year: 2005
Title: Structure and activity of the atypical serine kinase Rio1.
Authors: Laronde-Leblanc, N. / Guszczynski, T. / Copeland, T. / Wlodawer, A.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2005
Title: Pathological crystallography: case studies of several unusual macromolecular crystals.
Authors: Dauter, Z. / Botos, I. / Laronde-Leblanc, N. / Wlodawer, A.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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 1.6Oct 30, 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 kinase
B: Rio1 kinase
C: Rio1 kinase
D: Rio1 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,86212
Polymers122,6144
Non-polymers2,2488
Water16,502916
1
A: Rio1 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2163
Polymers30,6541
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rio1 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2163
Polymers30,6541
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rio1 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2163
Polymers30,6541
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rio1 kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2163
Polymers30,6541
Non-polymers5622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.306, 80.373, 121.320
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rio1 kinase


Mass: 30653.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: Rio1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta PLysS / References: UniProt: O28471
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.3
Details: PEG 4000, Ammonium Sulfate, MES, pH 6.3, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9686 / Wavelength: 0.9686 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / 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: 2→30 Å / Num. all: 69295 / Num. obs: 63199 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.106 / Net I/σ(I): 11.2

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Processing

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

1ztf


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.634 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 3196 5.1 %RANDOM
Rwork0.17702 ---
obs0.18067 60003 91.19 %-
all-62837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.419 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å2-0.07 Å2
2--2.95 Å20 Å2
3----1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.223 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7835 0 128 916 8879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6792.00110914
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61724.237380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.077151500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8211551
X-RAY DIFFRACTIONr_chiral_restr0.1120.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025964
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.24319
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25582
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2887
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2142
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.276
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2051.54977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6627708
X-RAY DIFFRACTIONr_scbond_it3.0433611
X-RAY DIFFRACTIONr_scangle_it4.5014.53206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 196 -
Rwork0.185 3562 -
obs--73.13 %

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