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- PDB-2r5t: Crystal Structure of Inactive Serum and Glucocorticoid- Regulated... -

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Basic information

Entry
Database: PDB / ID: 2r5t
TitleCrystal Structure of Inactive Serum and Glucocorticoid- Regulated Kinase 1 in Complex with AMP-PNP
ComponentsSerine/threonine-protein kinase Sgk1
KeywordsTRANSFERASE / AGC Protein Kinase / Apoptosis / ATP-binding / Cytoplasm / Endoplasmic reticulum / Nucleotide-binding / Nucleus / Phosphorylation / Serine/threonine-protein kinase / Ubl conjugation
Function / homology
Function and homology information


regulation of gastric acid secretion / renal sodium ion absorption / Transcriptional Regulation by MECP2 / positive regulation of transporter activity / cellular response to aldosterone / regulation of catalytic activity / NGF-stimulated transcription / chloride channel regulator activity / regulation of DNA-binding transcription factor activity / sodium ion transport ...regulation of gastric acid secretion / renal sodium ion absorption / Transcriptional Regulation by MECP2 / positive regulation of transporter activity / cellular response to aldosterone / regulation of catalytic activity / NGF-stimulated transcription / chloride channel regulator activity / regulation of DNA-binding transcription factor activity / sodium ion transport / calcium channel regulator activity / sodium channel regulator activity / potassium channel regulator activity / long-term memory / regulation of cell migration / protein serine/threonine/tyrosine kinase activity / neuron projection morphogenesis / regulation of signal transduction by p53 class mediator / regulation of cell growth / Stimuli-sensing channels / regulation of blood pressure / Regulation of TP53 Degradation / PIP3 activates AKT signaling / regulation of cell population proliferation / regulation of apoptotic process / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / endoplasmic reticulum membrane / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...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. / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase Sgk1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsZhao, B. / Lehr, R. / Smallwood, A.M. / Ho, T.F. / Maley, K. / Randall, T. / Head, M.S. / Koretke, K.K. / Schnackenberg, C.G.
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structure of the kinase domain of serum and glucocorticoid-regulated kinase 1 in complex with AMP PNP.
Authors: Zhao, B. / Lehr, R. / Smallwood, A.M. / Ho, T.F. / Maley, K. / Randall, T. / Head, M.S. / Koretke, K.K. / Schnackenberg, C.G.
History
DepositionSep 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Sgk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9304
Polymers42,3031
Non-polymers6273
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine/threonine-protein kinase Sgk1
hetero molecules

A: Serine/threonine-protein kinase Sgk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8608
Polymers84,6072
Non-polymers1,2536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area4950 Å2
MethodPISA
3
A: Serine/threonine-protein kinase Sgk1
hetero molecules

A: Serine/threonine-protein kinase Sgk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8608
Polymers84,6072
Non-polymers1,2536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area4270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.873, 97.873, 147.848
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-700-

SO4

21A-854-

HOH

31A-887-

HOH

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Components

#1: Protein Serine/threonine-protein kinase Sgk1 / Serum/glucocorticoid-regulated kinase 1


Mass: 42303.320 Da / Num. of mol.: 1 / Mutation: S74A, S78A, S397A, S401A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SGK, SGK1 / Production host: baculovirus
References: UniProt: O00141, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG 3350, LiSO4, pH 8.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 32802 / Num. obs: 32800 / % possible obs: 99.9 % / Redundancy: 16.2 % / Rsym value: 0.056 / Net I/σ(I): 53.9
Reflection shellHighest resolution: 1.9 Å / Redundancy: 16.2 % / Mean I/σ(I) obs: 53.9 / Num. unique all: 29141 / Rsym value: 0.056 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0006refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.572 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1825 5.9 %RANDOM
Rwork0.191 ---
obs0.193 30966 92.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.821 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.46 Å20 Å2
2--0.91 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 37 207 2511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222368
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9773222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5655282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1423.832107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6021510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021808
X-RAY DIFFRACTIONr_nbd_refined0.1940.21061
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2195
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.226
X-RAY DIFFRACTIONr_mcbond_it0.5231.51457
X-RAY DIFFRACTIONr_mcangle_it0.84722279
X-RAY DIFFRACTIONr_scbond_it1.40231040
X-RAY DIFFRACTIONr_scangle_it2.0664.5943
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 134 -
Rwork0.237 1739 -
all-1873 -
obs--76.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
118.43953.06576.993914.1581-3.39286.6585-0.15880.98781.3982-0.39330.5930.9559-1.1232-0.3986-0.43420.3903-0.233-0.03870.06620.11850.123134.992551.628675.1701
26.5349-3.6486-5.43937.977616.732519.7595-0.2702-0.1481-0.1895-2.14591.2621-2.0788-0.82771.9062-0.99190.3396-0.40740.0860.19420.00810.249346.678945.61965.5231
324.7549-7.1715-5.35693.14525.073212.774-0.13012.11010.6168-1.1480.15570.3688-1.337-0.5339-0.02560.6287-0.47510.04980.27040.05920.141635.294637.124461.6544
455.553219.05-8.099113.3946-4.664616.6522-0.459-0.6319-0.0677-0.1309-0.0483-1.9120.26731.18160.50720.3787-0.32530.0830.2141-0.14880.329350.21839.572769.1961
515.2552-11.30598.444120.2311-8.72029.09450.09340.64970.6555-0.9441-0.10641.43170.2758-0.84620.01310.5579-0.4342-0.14770.28890.03190.197730.645746.876163.5591
61.83761.2111-1.32168.84944.63074.7099-0.0160.21380.1511-0.3590.21210.1288-0.9119-0.0463-0.19610.2036-0.2526-0.0016-0.07130.0151-0.139432.097637.910779.2753
75.17362.5476-1.28618.53343.97396.1-0.51930.59420.4603-1.61110.8108-0.1596-1.03810.0845-0.29150.507-0.43310.01020.1033-0.009-0.084639.055244.330769.3109
80.98730.3742-0.73224.08621.82023.87250.09050.00620.0361-0.3652-0.0416-0.1973-0.79520.5129-0.049-0.0584-0.156-0.0311-0.13380.0152-0.168230.535324.871174.6616
95.40343.9424.843812.81499.696515.1698-0.4922-0.90461.6343-0.9766-0.1681-0.0935-3.082-0.35490.66030.50850.0116-0.14670.0869-0.2050.358120.07236.972360.8787
100.8837-0.00110.50831.4769-0.12544.6442-0.0219-0.06970.05870.1938-0.08250.0041-0.49640.04950.1044-0.1611-0.0272-0.0266-0.2307-0.004-0.148919.682820.770775.488
1113.1465-9.39748.18586.7175-5.85145.097-0.19811.7776-0.9955-0.78740.53351.4841-1.69610.4932-0.33540.5389-0.4663-0.02210.1309-0.02860.051532.801333.491766.3851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA82 - 9024 - 32
2X-RAY DIFFRACTION2AA91 - 10233 - 44
3X-RAY DIFFRACTION3AA103 - 11445 - 56
4X-RAY DIFFRACTION4AA115 - 12557 - 67
5X-RAY DIFFRACTION5AA126 - 13568 - 77
6X-RAY DIFFRACTION6AA149 - 16191 - 103
7X-RAY DIFFRACTION7AA162 - 179104 - 121
8X-RAY DIFFRACTION8AA180 - 243122 - 185
9X-RAY DIFFRACTION9AA244 - 258186 - 200
10X-RAY DIFFRACTION10AA259 - 378201 - 320
11X-RAY DIFFRACTION11AD5001

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