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- PDB-3ggf: Crystal structure of human Serine/threonine-protein kinase MST4 i... -

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Basic information

Entry
Database: PDB / ID: 3ggf
TitleCrystal structure of human Serine/threonine-protein kinase MST4 in complex with an quinazolin
ComponentsSerine/threonine-protein kinase MST4
KeywordsTRANSFERASE / Serine/threonine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC / Apoptosis / ATP-binding / Golgi apparatus / Kinase / Magnesium / Metal-binding / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


microvillus assembly / FAR/SIN/STRIPAK complex / vesicle membrane / Golgi-associated vesicle / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cell periphery / cellular response to oxidative stress / regulation of apoptotic process ...microvillus assembly / FAR/SIN/STRIPAK complex / vesicle membrane / Golgi-associated vesicle / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cell periphery / cellular response to oxidative stress / regulation of apoptotic process / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / apical plasma membrane / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
MST4, kinase domain / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain ...MST4, kinase domain / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-GVD / Serine/threonine-protein kinase 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChaikuad, A. / Rellos, P. / Eidarus, S. / Das, S. / Pike, A.C.W. / Sethi, R. / Fedorov, O. / Savitsky, P. / Roos, A.K. / Filippakopoulos, P. ...Chaikuad, A. / Rellos, P. / Eidarus, S. / Das, S. / Pike, A.C.W. / Sethi, R. / Fedorov, O. / Savitsky, P. / Roos, A.K. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Structural comparison of human mammalian ste20-like kinases
Authors: Record, C.J. / Chaikuad, A. / Rellos, P. / Das, S. / Pike, A.C. / Fedorov, O. / Marsden, B.D. / Knapp, S. / Lee, W.H.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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_ncs_dom_lim / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Serine/threonine-protein kinase MST4
B: Serine/threonine-protein kinase MST4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,27111
Polymers67,7222
Non-polymers1,5509
Water2,630146
1
A: Serine/threonine-protein kinase MST4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6926
Polymers33,8611
Non-polymers8315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase MST4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5795
Polymers33,8611
Non-polymers7194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-68 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.920, 91.250, 108.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEU1AA18 - 2719 - 28
21ALAALALEULEU1BB18 - 2719 - 28
12GLUGLUILEILE3AA28 - 4229 - 43
22GLUGLUILEILE3BB28 - 4229 - 43
13ASNASNVALVAL4AA44 - 4945 - 50
23ASNASNVALVAL4BB44 - 4945 - 50
14VALVALSERSER2AA50 - 7951 - 80
24VALVALSERSER2BB50 - 7951 - 80
15SERSERPHEPHE1AA80 - 16381 - 164
25SERSERPHEPHE1BB80 - 16381 - 164
16GLYGLYPHEPHE4AA164 - 179165 - 180
26GLYGLYPHEPHE4BB164 - 179165 - 180
17VALVALGLUGLU1AA180 - 297181 - 298
27VALVALGLUGLU1BB180 - 297181 - 298

NCS ensembles :
ID
1
2
3
4
5
6
7
DetailsAUTHOR SUGGESTS THAT DIMERIC IS AN INACTIVE FORM

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Components

#1: Protein Serine/threonine-protein kinase MST4 / Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / MST-4 / Serine/threonine-protein ...Mammalian STE20-like protein kinase 4 / STE20-like kinase MST4 / MST-4 / Serine/threonine-protein kinase MASK / Mst3 and SOK1-related kinase


Mass: 33860.766 Da / Num. of mol.: 2 / Fragment: protein kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MST4, MASK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: Q9P289, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GVD / [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE


Mass: 381.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19N7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 49.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12%w/v PEG 3350; 0.005M CdCl2; 0.1M HEPES, pH7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.88 Å
DetectorType: MAR225 CCD / Detector: CCD / Date: Jan 30, 2009 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.35→46.78 Å / Num. all: 28094 / Num. obs: 28094 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 9
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0085refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CKX

3ckx


Resolution: 2.35→46.78 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 15.297 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27698 1408 5 %RANDOM
Rwork0.21879 ---
obs0.22168 26636 99.93 %-
all-28044 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.182 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.55 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.334 Å
Refinement stepCycle: LAST / Resolution: 2.35→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 65 146 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224470
X-RAY DIFFRACTIONr_bond_other_d0.0030.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.996014
X-RAY DIFFRACTIONr_angle_other_deg0.9513.0027470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49425.027187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5715798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7881516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214869
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02855
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.5306
X-RAY DIFFRACTIONr_mcbond_other0.2551.5126
X-RAY DIFFRACTIONr_mcangle_it1.8432497
X-RAY DIFFRACTIONr_scbond_it2.5483177
X-RAY DIFFRACTIONr_scangle_it4.5434.5157
X-RAY DIFFRACTIONr_rigid_bond_restr6.5933
X-RAY DIFFRACTIONr_sphericity_free5.55833
X-RAY DIFFRACTIONr_sphericity_bonded17.27637
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A137tight positional0.020.05
21A86tight positional0.040.05
41A174tight positional0.040.05
51A1143tight positional0.050.05
71A1629tight positional0.060.05
31A86medium positional0.510.5
41A179medium positional0.040.5
61A48medium positional0.420.5
21A96loose positional0.035
12B137tight thermal0.110.5
22B86tight thermal0.140.5
42B174tight thermal0.20.5
52B1143tight thermal0.190.5
72B1629tight thermal0.180.5
32B86medium thermal1.842
42B179medium thermal0.172
62B48medium thermal2.062
22B96loose thermal0.1310
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 104 -
Rwork0.281 1947 -
obs--100 %
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)
121.30155.5153-11.699623.0802-7.359412.93030.6569-1.23320.536-0.8881-0.42390.9822-0.868-0.1517-0.2330.16360.0754-0.0540.2-0.06980.055889.031-3.95380.99
21.50920.5449-0.45191.0688-1.13591.6687-0.1029-0.08910.01110.0277-0.1-0.1952-0.27070.0240.20280.16820.0452-0.02320.0338-0.00960.117891.287-9.98693.816
31.5053-0.0331-0.11771.70580.19531.7603-0.0787-0.16010.02750.16910.0527-0.0642-0.1050.13960.02590.09890.01890.0010.03140.01240.133883.948-17.613109.279
418.9813.32895.598119.84578.671414.39981.1413-0.0224-0.9531-0.2434-0.3417-1.63971.12971.2944-0.79970.36070.23320.00280.2311-0.00090.157966.6534.49183.731
51.0483-0.23870.10152.37761.49353.1784-0.03690.0617-0.0394-0.2218-0.07550.14750.26820.21340.11240.18760.0674-0.00370.03660.00430.167761.5410.65295.686
62.7635-1.36131.07423.9275-0.10531.3077-0.0372-0.00830.116-0.2334-0.0246-0.0760.0005-0.05710.06180.08180.00330.0110.0041-0.00810.097670.46518.956111.343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 33
2X-RAY DIFFRACTION2A34 - 140
3X-RAY DIFFRACTION3A141 - 300
4X-RAY DIFFRACTION4B18 - 37
5X-RAY DIFFRACTION5B38 - 176
6X-RAY DIFFRACTION6B177 - 297

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