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- PDB-8wsw: The Crystal Structure of LIMK2a from Biortus -

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Basic information

Entry
Database: PDB / ID: 8wsw
TitleThe Crystal Structure of LIMK2a from Biortus
ComponentsLIM domain kinase 2
KeywordsTRANSFERASE / Kinase / Serine/threonine-protein kinase / ATP-binding / Metal-binding / Nucleotide-binding / Zinc
Function / homology
Function and homology information


cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / phosphorylation / EPHB-mediated forward signaling ...cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / phosphorylation / EPHB-mediated forward signaling / mitotic spindle / positive regulation of protein localization to nucleus / actin cytoskeleton organization / spermatogenesis / eukaryotic translation initiation factor 2alpha kinase activity / 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 / positive regulation of protein phosphorylation / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / ATP binding / nucleus / metal ion binding / 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 / 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
Chem-LH0 / LIM domain kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Pan, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of LIMK2a from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Pan, W.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIM domain kinase 2
B: LIM domain kinase 2
C: LIM domain kinase 2
D: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,16826
Polymers138,3264
Non-polymers2,84222
Water5,423301
1
A: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4479
Polymers34,5811
Non-polymers8668
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint1 kcal/mol
Surface area13710 Å2
MethodPISA
2
B: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2616
Polymers34,5811
Non-polymers6805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13660 Å2
MethodPISA
3
C: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2616
Polymers34,5811
Non-polymers6805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13740 Å2
MethodPISA
4
D: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1995
Polymers34,5811
Non-polymers6174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.223, 104.175, 96.443
Angle α, β, γ (deg.)90.000, 116.683, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 330 - 632 / Label seq-ID: 1 - 303

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
32AA
42CC
53AA
63DD
74BB
84CC
95BB
105DD
116CC
126DD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
LIM domain kinase 2 / LIMK-2


Mass: 34581.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK2 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: P53671, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-LH0 / ~{N}-[5-[2-[2,6-bis(chloranyl)phenyl]-5-[bis(fluoranyl)methyl]pyrazol-3-yl]-1,3-thiazol-2-yl]-2-methyl-propanamide


Mass: 431.287 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H14Cl2F2N4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES ,7.3,10% w/vPEG 8000, 8%v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.35 Å / Num. obs: 53195 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.58 Å / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4615

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.787 / SU ML: 0.224 / Cross valid method: FREE R-VALUE / ESU R: 0.465 / ESU R Free: 0.284
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2563 2728 5.13 %
Rwork0.2093 50447 -
all0.212 --
obs-53175 98.443 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.277 Å2
Baniso -1Baniso -2Baniso -3
1--3.695 Å20 Å21.732 Å2
2---3.07 Å20 Å2
3---3.338 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8948 0 180 301 9429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139375
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179067
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.6512654
X-RAY DIFFRACTIONr_angle_other_deg1.11.57820974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23451128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97322.821429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.654151669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.071541
X-RAY DIFFRACTIONr_chiral_restr0.050.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022010
X-RAY DIFFRACTIONr_nbd_refined0.1910.21779
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.28066
X-RAY DIFFRACTIONr_nbtor_refined0.1570.24509
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.24338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2278
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.29
X-RAY DIFFRACTIONr_nbd_other0.170.255
X-RAY DIFFRACTIONr_mcbond_it3.0876.0574509
X-RAY DIFFRACTIONr_mcbond_other3.0876.0574508
X-RAY DIFFRACTIONr_mcangle_it5.0549.0715629
X-RAY DIFFRACTIONr_mcangle_other5.0549.0725630
X-RAY DIFFRACTIONr_scbond_it3.1216.4924866
X-RAY DIFFRACTIONr_scbond_other3.1216.4934867
X-RAY DIFFRACTIONr_scangle_it5.2139.5617022
X-RAY DIFFRACTIONr_scangle_other5.2139.5617023
X-RAY DIFFRACTIONr_lrange_it8.06269.98810180
X-RAY DIFFRACTIONr_lrange_other8.06669.98510157
X-RAY DIFFRACTIONr_ncsr_local_group_10.0490.059010
X-RAY DIFFRACTIONr_ncsr_local_group_20.0620.058866
X-RAY DIFFRACTIONr_ncsr_local_group_30.0610.058895
X-RAY DIFFRACTIONr_ncsr_local_group_40.0570.058894
X-RAY DIFFRACTIONr_ncsr_local_group_50.0580.058925
X-RAY DIFFRACTIONr_ncsr_local_group_60.0530.058908
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.048830.05009
12BX-RAY DIFFRACTIONLocal ncs0.048830.05009
23AX-RAY DIFFRACTIONLocal ncs0.061860.05009
24CX-RAY DIFFRACTIONLocal ncs0.061860.05009
35AX-RAY DIFFRACTIONLocal ncs0.060910.05009
36DX-RAY DIFFRACTIONLocal ncs0.060910.05009
47BX-RAY DIFFRACTIONLocal ncs0.056770.05009
48CX-RAY DIFFRACTIONLocal ncs0.056770.05009
59BX-RAY DIFFRACTIONLocal ncs0.058290.05009
510DX-RAY DIFFRACTIONLocal ncs0.058290.05009
611CX-RAY DIFFRACTIONLocal ncs0.053040.05009
612DX-RAY DIFFRACTIONLocal ncs0.053040.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.4231960.3433711X-RAY DIFFRACTION99.087
2.565-2.6350.3581880.3033608X-RAY DIFFRACTION97.7091
2.635-2.7110.3252160.293504X-RAY DIFFRACTION99.2
2.711-2.7950.3761860.273472X-RAY DIFFRACTION99.3212
2.795-2.8860.2991540.2533334X-RAY DIFFRACTION99.1754
2.886-2.9880.2961580.2533258X-RAY DIFFRACTION99.187
2.988-3.10.2941710.2453155X-RAY DIFFRACTION99.1356
3.1-3.2270.2881590.2432989X-RAY DIFFRACTION98.9315
3.227-3.370.2671710.2382859X-RAY DIFFRACTION98.6007
3.37-3.5340.2581490.2272712X-RAY DIFFRACTION97.7785
3.534-3.7250.2651770.1982561X-RAY DIFFRACTION98.0659
3.725-3.950.2261270.1922431X-RAY DIFFRACTION97.5219
3.95-4.2220.2151290.1722332X-RAY DIFFRACTION98.756
4.222-4.560.1911060.1552179X-RAY DIFFRACTION98.4489
4.56-4.9940.21200.1571966X-RAY DIFFRACTION98.3498
4.994-5.5810.2331060.181792X-RAY DIFFRACTION98.1386
5.581-6.440.235780.1911603X-RAY DIFFRACTION96.9435
6.44-7.8760.169600.1461345X-RAY DIFFRACTION96.6965
7.876-11.0920.188500.141040X-RAY DIFFRACTION96.5456
11.092-48.350.268270.229596X-RAY DIFFRACTION94.5372

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