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- PDB-6bxi: X-ray crystal structure of NDR1 kinase domain -

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Basic information

Entry
Database: PDB / ID: 6bxi
TitleX-ray crystal structure of NDR1 kinase domain
ComponentsSerine/threonine-protein kinase 38Serine/threonine-specific protein kinase
KeywordsTRANSFERASE / kinase fold with atypically long activation segment
Function / homology
Function and homology information


postsynapse organization / mitogen-activated protein kinase kinase kinase binding / RHOBTB1 GTPase cycle / RHOBTB2 GTPase cycle / negative regulation of MAP kinase activity / protein modification process / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / protein phosphorylation ...postsynapse organization / mitogen-activated protein kinase kinase kinase binding / RHOBTB1 GTPase cycle / RHOBTB2 GTPase cycle / negative regulation of MAP kinase activity / protein modification process / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / magnesium ion binding / ATP binding / nucleus / 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. / 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 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. / 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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase 38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsXiong, S. / Sicheri, F.
CitationJournal: Structure / Year: 2018
Title: Structural Basis for Auto-Inhibition of the NDR1 Kinase Domain by an Atypically Long Activation Segment.
Authors: Xiong, S. / Lorenzen, K. / Couzens, A.L. / Templeton, C.M. / Rajendran, D. / Mao, D.Y.L. / Juang, Y.C. / Chiovitti, D. / Kurinov, I. / Guettler, S. / Gingras, A.C. / Sicheri, F.
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 38
B: Serine/threonine-protein kinase 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5686
Polymers77,5072
Non-polymers1,0614
Water7,945441
1
A: Serine/threonine-protein kinase 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2843
Polymers38,7531
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine/threonine-protein kinase 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2843
Polymers38,7531
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.191, 117.967, 95.044
Angle α, β, γ (deg.)90.00, 124.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-776-

HOH

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Components

#1: Protein Serine/threonine-protein kinase 38 / Serine/threonine-specific protein kinase / NDR1 protein kinase / Nuclear Dbf2-related kinase 1


Mass: 38753.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK38, NDR1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15208, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 4 M ammonium acetate, 0.1 M Bis-Tris propane pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→48.071 Å / Num. obs: 220717 / % possible obs: 98 % / Redundancy: 3.5 % / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.45 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.2→48.071 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 20.58
RfactorNum. reflection% reflection
Rfree0.2123 2554 5.09 %
Rwork0.1705 --
obs0.1726 50219 93.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5367 0 64 441 5872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085571
X-RAY DIFFRACTIONf_angle_d1.1847540
X-RAY DIFFRACTIONf_dihedral_angle_d14.6642065
X-RAY DIFFRACTIONf_chiral_restr0.055817
X-RAY DIFFRACTIONf_plane_restr0.006950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1999-2.24220.26561130.22042341X-RAY DIFFRACTION82
2.2422-2.28790.27351390.2152521X-RAY DIFFRACTION90
2.2879-2.33770.23141450.20512626X-RAY DIFFRACTION93
2.3377-2.39210.23371450.20612669X-RAY DIFFRACTION94
2.3921-2.45190.24871670.20092677X-RAY DIFFRACTION95
2.4519-2.51820.25111500.19662654X-RAY DIFFRACTION94
2.5182-2.59230.24231520.19792647X-RAY DIFFRACTION95
2.5923-2.67590.2091290.18832755X-RAY DIFFRACTION97
2.6759-2.77160.21231590.17492723X-RAY DIFFRACTION96
2.7716-2.88250.23761510.17482698X-RAY DIFFRACTION95
2.8825-3.01370.23491500.17412670X-RAY DIFFRACTION95
3.0137-3.17250.22411290.17172679X-RAY DIFFRACTION94
3.1725-3.37130.22421310.16962749X-RAY DIFFRACTION96
3.3713-3.63150.17321440.15922696X-RAY DIFFRACTION95
3.6315-3.99680.19241550.14372620X-RAY DIFFRACTION93
3.9968-4.57470.17871280.13692678X-RAY DIFFRACTION93
4.5747-5.76210.19381310.15732655X-RAY DIFFRACTION93
5.7621-48.08270.19451360.16722607X-RAY DIFFRACTION90
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)
11.9283-0.2803-0.42821.18810.1931.0745-0.089-0.06640.46710.24270.0082-0.5319-0.13270.2430.00320.21820.0526-0.05760.3058-0.01920.3507174.132713.21430.4983
21.02950.22670.58111.18680.34991.49060.0354-0.0795-0.01890.1605-0.0018-0.08220.18510.0554-0.00860.24410.04190.00270.16930.0030.1747159.18666.51827.5323
31.584-0.21180.25721.64630.50171.3724-0.08360.19240.2605-0.384-0.15930.2572-0.302-0.34650.15340.31160.0139-0.05820.3111-0.00160.3049145.717919.572414.9037
41.0064-0.08950.23481.63570.52061.85230.0212-0.05470.0638-0.0192-0.15590.17390.1093-0.28040.11970.1696-0.00430.00350.2102-0.03690.1866142.63527.920915.9862
52.48940.40830.45281.35780.08241.33120.04930.3448-0.17210.10520.0989-0.22590.29460.1948-0.1490.37380.1030.03190.2502-0.01540.198164.705-1.877916.9393
62.02510.72020.02211.8976-0.03821.6304-0.09180.209-0.3159-0.24580.1749-0.31610.14190.1821-0.07710.2719-0.04490.04310.2653-0.01150.2886167.0841-16.9005-33.6154
70.876-0.2268-0.44361.13910.18971.27780.00810.08370.0091-0.12640.0051-0.0603-0.1430.0654-0.0190.1901-0.0403-0.0070.17230.00230.1854155.5648-7.3689-27.8354
81.71610.5347-0.54442.1123-0.34531.5124-0.0053-0.0924-0.23210.0608-0.27650.36870.2864-0.28460.20620.2731-0.05310.02760.2782-0.07230.3127141.687-23.2467-23.0011
91.2867-0.80530.19842.30421.08222.5103-0.3192-0.3169-0.21740.64650.0410.14980.1296-0.0690.23790.2861-0.00960.04150.21350.03680.206148.748-20.4336-9.7493
100.6731-0.0916-0.17471.49740.44051.36970.02370.0118-0.04280.0322-0.17390.2703-0.1285-0.2720.14520.17910.0087-0.00510.2344-0.04540.1928139.1598-8.5524-15.0149
112.43520.04-0.87150.96760.80131.36770.2512-0.05070.0769-0.3570.0926-0.1997-0.11350.2565-0.28780.3612-0.0685-0.06050.2576-0.02170.2269162.8407-0.7374-19.1071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 228 )
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 273 )
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 382 )
5X-RAY DIFFRACTION5chain 'A' and (resid 383 through 414 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 127 )
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 228 )
8X-RAY DIFFRACTION8chain 'B' and (resid 229 through 256 )
9X-RAY DIFFRACTION9chain 'B' and (resid 257 through 290 )
10X-RAY DIFFRACTION10chain 'B' and (resid 291 through 382 )
11X-RAY DIFFRACTION11chain 'B' and (resid 383 through 414 )

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