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- PDB-4l3l: Crystal structures of human p70S6K1 kinase domain (Zinc anomalous) -

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Basic information

Entry
Database: PDB / ID: 4l3l
TitleCrystal structures of human p70S6K1 kinase domain (Zinc anomalous)
ComponentsRPS6KB1 protein
KeywordsTRANSFERASE / Protein kinase
Function / homology
Function and homology information


long-chain fatty acid import into cell / negative regulation of TORC2 signaling / cellular response to nutrient / TORC1 signaling / phosphatidylinositol-mediated signaling / germ cell development / TOR signaling / mTORC1-mediated signalling / positive regulation of translational initiation / cellular response to dexamethasone stimulus ...long-chain fatty acid import into cell / negative regulation of TORC2 signaling / cellular response to nutrient / TORC1 signaling / phosphatidylinositol-mediated signaling / germ cell development / TOR signaling / mTORC1-mediated signalling / positive regulation of translational initiation / cellular response to dexamethasone stimulus / behavioral fear response / positive regulation of TORC1 signaling / protein serine/threonine/tyrosine kinase activity / negative regulation of insulin receptor signaling pathway / positive regulation of mitotic cell cycle / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / response to nutrient levels / G1/S transition of mitotic cell cycle / modulation of chemical synaptic transmission / peptidyl-serine phosphorylation / cellular response to growth factor stimulus / cellular response to type II interferon / cellular response to insulin stimulus / mitochondrial outer membrane / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / glutamatergic synapse / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Ribosomal protein S6 kinase / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Similarity search - Domain/homology
Chem-5FI / Ribosomal protein S6 kinase beta-1 / Ribosomal protein S6 kinase beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, J. / Zhong, C. / Ding, J.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structures of S6K1 provide insights into the regulation mechanism of S6K1 by the hydrophobic motif
Authors: Wang, J. / Zhong, C. / Wang, F. / Qu, F. / Ding, J.
History
DepositionJun 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RPS6KB1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7933
Polymers34,3371
Non-polymers4562
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.408, 69.408, 143.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is monomer

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Components

#1: Protein RPS6KB1 protein / Ribosomal protein S6 kinase beta-1 / Ribosomal protein S6 kinase / 70kDa / polypeptide 1 / isoform CRA_c


Mass: 34337.094 Da / Num. of mol.: 1 / Fragment: UNP residues 88-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6KB1, hCG_1815774 / Plasmid: pFastBacHTB / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Spodoptera frugiperda / References: UniProt: Q7Z721, UniProt: P23443*PLUS
#2: Chemical ChemComp-5FI / 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole


Mass: 390.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21F3N6
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.88 % / Mosaicity: 0.452 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5M sodium formate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.2826 Å
DetectorType: CCD ADSC unsupported-q315 / Detector: CCD / Date: May 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionRedundancy: 8.9 % / Av σ(I) over netI: 22.51 / Number: 181839 / Rmerge(I) obs: 0.121 / Χ2: 1.82 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 20480 / % possible obs: 96.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525084.510.082.337.3
3.594.5284.910.0962.87.3
3.143.5996.910.1082.5158.4
2.853.1499.110.1131.9939.1
2.652.8599.810.1341.8149.3
2.492.6510010.1661.79.4
2.372.4910010.21.6079.4
2.262.3710010.2561.4899.4
2.182.2610010.3261.3369.4
2.12.1810010.431.1439.4
ReflectionResolution: 2.1→50 Å / Num. obs: 20480 / % possible obs: 96.3 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.121 / Χ2: 1.817 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.189.40.4320731.1431100
2.18-2.269.40.32620521.3361100
2.26-2.379.40.25620721.4891100
2.37-2.499.40.221091.6071100
2.49-2.659.40.16620861.71100
2.65-2.859.30.13421011.814199.8
2.85-3.149.10.11320951.993199.1
3.14-3.598.40.10820712.515196.9
3.59-4.527.30.09618452.8184.9
4.52-507.30.0819762.33184.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A62

3a62


Resolution: 2.1→46.48 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.031 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 1033 5.1 %RANDOM
Rwork0.2065 ---
obs0.2085 20329 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.45 Å2 / Biso mean: 56.1127 Å2 / Biso min: 27.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0 Å2-0 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 29 61 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192388
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9883221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1265290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26423.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82615434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2231514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211771
X-RAY DIFFRACTIONr_rigid_bond_restr9.32632388
X-RAY DIFFRACTIONr_sphericity_free0535
X-RAY DIFFRACTIONr_sphericity_bonded19.46852403
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 79 -
Rwork0.203 1411 -
all-1490 -
obs--97.96 %
Refinement TLS params.Method: refined / Origin x: -12.0547 Å / Origin y: 20.0145 Å / Origin z: 4.8641 Å
111213212223313233
T0.0755 Å2-0.0026 Å20.0015 Å2-0.09 Å20.0019 Å2--0.0072 Å2
L0.1176 °2-0.0858 °20.0422 °2-0.3563 °2-0.0111 °2--0.0238 °2
S-0.0061 Å °0.0023 Å °0.0262 Å °0.0144 Å °-0.0016 Å °-0.0373 Å °-0.018 Å °0.0196 Å °0.0077 Å °

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