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- PDB-3s95: Crystal structure of the human LIMK1 kinase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3s95
TitleCrystal structure of the human LIMK1 kinase domain in complex with staurosporine
ComponentsLIM domain kinase 1
KeywordsTRANSFERASE/ANTIBIOTIC / Structural Genomics / Structural Genomics Consortium / SGC / Protein Kinase / LIM domain kinase / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


positive regulation of actin filament bundle assembly / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / axon extension / stress fiber assembly / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / ubiquitin ligase inhibitor activity / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction ...positive regulation of actin filament bundle assembly / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / axon extension / stress fiber assembly / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / ubiquitin ligase inhibitor activity / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / positive regulation of axon extension / positive regulation of stress fiber assembly / heat shock protein binding / EPHB-mediated forward signaling / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / nervous system development / lamellipodium / actin cytoskeleton organization / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / postsynapse / protein kinase activity / neuron projection / nuclear speck / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ubiquitin protein ligase binding / glutamatergic synapse / signal transduction / ATP binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
STAUROSPORINE / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBeltrami, A. / Chaikuad, A. / Daga, N. / Elkins, J.M. / Mahajan, P. / Savitsky, P. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / Fedorov, O. ...Beltrami, A. / Chaikuad, A. / Daga, N. / Elkins, J.M. / Mahajan, P. / Savitsky, P. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / Fedorov, O. / Allerston, C.K. / Yue, W.W. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the human LIMK1 kinase domain in complex with staurosporine
Authors: Beltrami, A. / Chaikuad, A. / Daga, N. / Elkins, J.M. / Mahajan, P. / Savitsky, P. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / Fedorov, O. / Allerston, C.K. / Yue, W.W. / Gileadi, O. / von ...Authors: Beltrami, A. / Chaikuad, A. / Daga, N. / Elkins, J.M. / Mahajan, P. / Savitsky, P. / Vollmar, M. / Krojer, T. / Muniz, J.R.C. / Fedorov, O. / Allerston, C.K. / Yue, W.W. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Bullock, A.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIM domain kinase 1
B: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,41522
Polymers71,9902
Non-polymers2,42520
Water10,485582
1
A: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,47114
Polymers35,9951
Non-polymers1,47613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9448
Polymers35,9951
Non-polymers9497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.160, 128.000, 131.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LIM domain kinase 1 / LIMK-1


Mass: 35994.773 Da / Num. of mol.: 2 / Fragment: kinase domain (residue 330-637)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK, LIMK1 / Plasmid: pFB-LIC-Bse / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P53667, non-specific serine/threonine protein kinase

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Non-polymers , 7 types, 602 molecules

#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 24% MPD, 0.1M Tris pH 7.2, 10mM Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2011
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→43.78 Å / Num. all: 105650 / Num. obs: 105524 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.2 / Num. unique all: 15293 / % possible all: 98.5

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YI6 and 2QO9

1yi6

2qo9


Resolution: 1.65→40.86 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.118 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18084 5270 5 %RANDOM
Rwork0.15544 ---
obs0.15673 100253 98.39 %-
all-105524 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.827 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---0.04 Å20 Å2
3----1.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 1.65→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4647 0 164 582 5393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225060
X-RAY DIFFRACTIONr_bond_other_d0.0010.023578
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9976861
X-RAY DIFFRACTIONr_angle_other_deg0.98738669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03822.814231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74115873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0481545
X-RAY DIFFRACTIONr_chiral_restr0.0980.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021065
X-RAY DIFFRACTIONr_mcbond_it3.00232963
X-RAY DIFFRACTIONr_mcbond_other0.85431187
X-RAY DIFFRACTIONr_mcangle_it4.8554812
X-RAY DIFFRACTIONr_scbond_it7.01382097
X-RAY DIFFRACTIONr_scangle_it9.704112028
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 395 -
Rwork0.318 7381 -
obs--98.96 %
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)
10.5992-1.0564-0.08023.59990.11750.35010.1330.1084-0.0381-0.4573-0.16960.06550.151-0.02310.03650.20520.0415-0.01990.10220.00590.029619.17865.696337.6561
20.5686-0.34540.00291.3445-0.24361.7116-0.00110.02890.09690.046-0.004-0.1473-0.14250.02480.00510.07750.0118-0.01250.07920.02480.06520.678828.831948.4551
32.92041.444-0.0780.8983-0.03170.4316-0.22610.3676-0.0518-0.17910.1912-0.0391-0.09740.10750.03490.1663-0.0641-0.00150.1512-0.00910.033947.529524.312372.7382
40.71130.14250.15591.02150.12051.54690.0003-0.01920.0550.0153-0.03510.0859-0.0289-0.17440.03480.0998-0.0015-0.02320.0706-0.00960.055124.37321.724282.5093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 0
2X-RAY DIFFRACTION1A330 - 512
3X-RAY DIFFRACTION2A513 - 637
4X-RAY DIFFRACTION3B-1 - 0
5X-RAY DIFFRACTION3B330 - 512
6X-RAY DIFFRACTION4B513 - 637

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