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- PDB-3ps4: PDZ domain from Human microtubule-associated serine/threonine-pro... -

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Basic information

Entry
Database: PDB / ID: 3ps4
TitlePDZ domain from Human microtubule-associated serine/threonine-protein kinase 1
ComponentsMicrotubule-associated serine/threonine-protein kinase 1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / KINASE / PDZ domain / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


cytoskeleton organization / brain development / microtubule binding / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / intracellular signal transduction / axon / protein phosphorylation / protein serine kinase activity ...cytoskeleton organization / brain development / microtubule binding / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / intracellular signal transduction / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / neuronal cell body / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Microtubule-associated serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsUgochukwu, E. / Wang, J. / Krojer, T. / Muniz, J.R.C. / Sethi, R. / Pike, A.C.W. / Roos, A. / Salah, E. / Cocking, R. / Savitsky, P. ...Ugochukwu, E. / Wang, J. / Krojer, T. / Muniz, J.R.C. / Sethi, R. / Pike, A.C.W. / Roos, A. / Salah, E. / Cocking, R. / Savitsky, P. / Doyle, D.A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Elkins, J.M. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: PDZ domain from Human microtubule-associated serine/threonine-protein kinase 1
Authors: Ugochukwu, E. / Wang, J. / Krojer, T. / Muniz, J.R.C. / Sethi, R. / Pike, A.C.W. / Roos, A. / Salah, E. / Cocking, R. / Savitsky, P. / Doyle, D.A. / von Delft, F. / Bountra, C. / Arrowsmith, ...Authors: Ugochukwu, E. / Wang, J. / Krojer, T. / Muniz, J.R.C. / Sethi, R. / Pike, A.C.W. / Roos, A. / Salah, E. / Cocking, R. / Savitsky, P. / Doyle, D.A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Elkins, J.M. / Structural Genomics Consortium (SGC)
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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 / 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_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: Microtubule-associated serine/threonine-protein kinase 1
B: Microtubule-associated serine/threonine-protein kinase 1
C: Microtubule-associated serine/threonine-protein kinase 1
D: Microtubule-associated serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3839
Polymers45,0514
Non-polymers3315
Water4,125229
1
A: Microtubule-associated serine/threonine-protein kinase 1
D: Microtubule-associated serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7886
Polymers22,5262
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-6 kcal/mol
Surface area9640 Å2
MethodPISA
2
B: Microtubule-associated serine/threonine-protein kinase 1
C: Microtubule-associated serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5953
Polymers22,5262
Non-polymers691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-10 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 79.326, 82.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Microtubule-associated serine/threonine-protein kinase 1 / Syntrophin-associated serine/threonine-protein kinase


Mass: 11262.806 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Fragment: unp residues 965-1057 / Gene: MAST1, KIAA0973 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: Q9Y2H9, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 25 w/v PEG_MME_2000 85 mM Imidazole pH 6.1, 15 mM Imidazole pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→57.26 Å / Num. all: 35617 / Num. obs: 35510 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 30.21 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.2 / Num. unique all: 5134 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2v90

2v90


Resolution: 1.85→25.48 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.9407 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1781 5.02 %RANDOM
Rwork0.194 ---
obs0.1956 35449 --
all-35449 --
Displacement parametersBiso mean: 36.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.9061 Å20 Å20 Å2
2---3.1083 Å20 Å2
3---2.2023 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: LAST / Resolution: 1.85→25.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 23 229 3160
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00930502
X-RAY DIFFRACTIONt_angle_deg1.0841722
X-RAY DIFFRACTIONt_dihedral_angle_d13452
X-RAY DIFFRACTIONt_trig_c_planes612
X-RAY DIFFRACTIONt_gen_planes4645
X-RAY DIFFRACTIONt_it305020
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion2.43
X-RAY DIFFRACTIONt_chiral_improper_torsion4145
X-RAY DIFFRACTIONt_ideal_dist_contact35874
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.257 135 4.7 %
Rwork0.2263 2740 -
all0.2277 2875 -
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)
11.17830.233-0.31523.76090.77182.1948-0.03310.0958-0.0118-0.15430.0585-0.138-0.11340.0179-0.02540.04840.06130.0258-0.003-0.0249-0.0411-2.2064-2.921-11.5136
21.3919-0.54951.18110.24742.781700.06290.0404-0.14990.1032-0.07-0.0517-0.04210.07850.00710.0229-0.0079-0.0112-0.0493-0.0012-0.0248-1.1329-0.6197-0.9599
31.17840.15171.11951.10821.27743.33560.1125-0.5191-0.00970.1371-0.18140.10280.1273-0.41190.06890.0355-0.03440.01830.0454-0.0042-0.0328-9.37153.75617.5047
42.2630.5614-0.21461.23370.19011.78460.07990.2708-0.0917-0.1009-0.0817-0.105-0.2897-0.20270.00180.02030.033-0.0028-0.0353-0.0097-0.0617-7.31372.8639-5.7218
50.01450.67071.34540.8661-0.80250.21040.0039-0.006-0.1860.1303-0.01670.16880.0267-0.14150.0128-0.0179-0.01990.02940.060.0102-0.021-15.2883-6.66591.1596
60-1.2336-2.46031.0473-0.59790.69040.032-0.1568-0.33830.0153-0.00820.01050.1979-0.0603-0.02380.0507-0.00910.0118-0.0170.00340.0515-6.1066-9.8552-0.1054
72.44531.3608-0.8520.926-0.96930.3183-0.03040.1531-0.0086-0.09-0.0194-0.094-0.00080.01930.04980.00510.0553-0.00580.0181-0.0292-0.033-8.3645-1.8083-8.3291
80.8906-2.04940.31640.00141.06210.0973-0.0153-0.04430.0553-0.05020.0422-0.0103-0.03990.0269-0.02690.1227-0.0323-0.0265-0.056-0.024-0.0586-4.667317.93913.7953
90.14-1.62131.09250.5014-0.15570.0565-0.0009-0.0387-0.0670.0305-0.0673-0.0030.06560.08910.06820.1568-0.0406-0.0442-0.0530.0184-0.0362-5.22668.7762-19.4905
104.12660.8134-0.0460.8319-0.71491.52390.12530.36560.0681-0.2204-0.0880.06560.0819-0.2431-0.0373-0.0587-0.00850.0459-0.0425-0.0099-0.0506-14.201819.4425-23.2075
110.34380.38740.22950.51570.1410.6009-0.0085-0.03420.03810.0651-0.00080.0140.01090.04150.00920.119-0.02970.0010.1218-0.13530.07972.471838.1123-15.3698
120.94071.12031.19422.86121.51.607-0.00450.01080.14790.0281-0.06630.02560.003-0.18810.0708-0.0233-0.05990.04-0.0677-0.0149-0.0291-11.702522.38-18.2791
135.51061.8226-0.02771.89950.26974.62770.17320.0495-0.13050.2629-0.0487-0.37840.41250.2384-0.12450.048-0.0166-0.0129-0.0450.009-0.001-6.699115.8809-20.5562
141.22192.5281.47691.3528-0.12561.15030.03030.26710.1287-0.187-0.0542-0.0753-0.1002-0.07380.0239-0.0169-0.0330.0415-0.03650.0412-0.0269-7.585623.4067-29.2446
152.70851.6035-0.8971.66881.94290.5487-0.040.2028-0.1616-0.09360.0648-0.05250.1451-0.0273-0.02480.0485-0.042-0.0305-0.0533-0.0192-0.0427-9.053812.6924-26.3544
160.23681.17021.1482.34070.509900.0286-0.01990.0134-0.06850.00340.03390.1899-0.0279-0.03210.0760.0033-0.01130.04720.0029-0.0126-10.51621.7467-3.6558
172.3952-1.44490.41161.6520.16910.5413-0.0303-0.00960.21560.05970.0241-0.1493-0.01660.05530.00610.0152-0.02550.0049-0.0208-0.06510.0069-16.385140.67071.4373
181.2158-0.812-0.33111.09391.53580.8293-0.00470.0687-0.0922-0.0851-0.0527-0.1383-0.12630.16750.0574-0.08580.00150.0535-0.02640.00040.0646-8.729227.4907-5.8177
190.3565-0.07660.002300.1780.3146-0.00140.01620.0123-0.06290.01260.00730.0160.0147-0.0111-0.0672-0.01070.05130.0902-0.14650.18117.419419.713-15.4369
202.4963-1.2084-1.34781.25041.15611.0719-0.01560.0854-0.12320.0197-0.123-0.24690.04130.10190.1387-0.07640.01420.0336-0.0013-0.00840.0372-12.219629.8531-6.5686
212.320.4294-1.41894.22660.06362.93120.01130.11630.1613-0.2541-0.2279-0.3852-0.22380.01120.2166-0.07570.0060.021-0.00170.02920.0387-11.444737.7935-6.6133
222.4081-1.48341.46683.53871.06061.1888-0.0207-0.12020.11590.152-0.0728-0.2478-0.03740.0610.0936-0.0059-0.0297-0.07230.0770.00610.0419-3.986733.25191.7325
230.8653-0.36311.53792.0386-1.45190.8902-0.0036-0.08270.2027-0.0388-0.0779-0.1177-0.0382-0.02260.0814-0.1193-0.08380.032-0.046-0.0534-0.0053-10.369241.0091-3.622
240.26320.12050.30930.3950.38690.6987-0.00520.07160.05570.0527-0.0464-0.0108-0.0970.04830.05160.02530.00040.05440.04260.0110.0471-15.616528.7329-22.1658
251.44970.6466-1.27770.877-0.30151.583-0.0389-0.18130.10920.11620.0917-0.1381-0.0018-0.08-0.0529-0.0364-0.01810.02620.1348-0.0478-0.1352-4.915913.646824.7198
260.5459-0.6635-0.61662.00631.37320.60440.0086-0.06350.3202-0.05690.055-0.1135-0.3087-0.0817-0.0636-0.03450.0167-0.0293-0.05-0.0141-0.0978-5.083416.86410.086
271.1163-0.7390.68540.22030.01460.8372-0.0202-0.0198-0.02250.027-0.0032-0.0035-0.0363-0.11250.0233-0.06110.1351-0.13230.302-0.13640.137-21.99818.0335-0.6518
280.2631.96881.73781.88972.40312.01010.0072-0.01750.0906-0.06370.06890.0067-0.1958-0.0092-0.076-0.06830.0127-0.0201-0.0135-0.0157-0.0497-0.865813.276111.6816
290.04571.1074-1.14132.00480.67843.74180.0664-0.20550.08130.3861-0.1417-0.01180.0329-0.16310.0753-0.0264-0.0001-0.01020.0604-0.0342-0.0549-3.973711.707618.2105
300.91430.3561.30910.1739-0.62840.5316-0.0048-0.11820.01020.0063-0.03730.1338-0.0566-0.11380.04220.01450.0815-0.03320.0544-0.0619-0.0299-15.144217.993113.3986
310.1574-0.5104-0.94512.1192-0.26750.39950.0053-0.02690.04180.0272-0.01370.0122-0.07110.03680.00840.20250.127-0.1002-0.0283-0.1120.0519-9.400924.469416.7863
320.5406-1.59112.72410.1793-0.85652.068-0.0267-0.29180.10710.05380.0282-0.02080.0098-0.0929-0.0016-0.0603-0.02590.08650.0344-0.063-0.0922-5.198112.217821.2528
331.2422-0.95591.26060.49071.37140.3006-0.0205-0.1234-0.0660.0190.0621-0.0730.01730.0038-0.04160.0353-0.0392-0.00920.01790.0045-0.02910.2725-2.36036.9798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|966 - 976}A966 - 976
2X-RAY DIFFRACTION2{A|977 - 982}A977 - 982
3X-RAY DIFFRACTION3{A|983 - 1009}A983 - 1009
4X-RAY DIFFRACTION4{A|1010 - 1024}A1010 - 1024
5X-RAY DIFFRACTION5{A|1025 - 1032}A1025 - 1032
6X-RAY DIFFRACTION6{A|1033 - 1042}A1033 - 1042
7X-RAY DIFFRACTION7{A|1043 - 1053}A1043 - 1053
8X-RAY DIFFRACTION8{A|1054 - 1061}A1054 - 1061
9X-RAY DIFFRACTION9{B|965 - 970}B965 - 970
10X-RAY DIFFRACTION10{B|971 - 986}B971 - 986
11X-RAY DIFFRACTION11{B|987 - 992}B987 - 992
12X-RAY DIFFRACTION12{B|993 - 1009}B993 - 1009
13X-RAY DIFFRACTION13{B|1010 - 1029}B1010 - 1029
14X-RAY DIFFRACTION14{B|1030 - 1040}B1030 - 1040
15X-RAY DIFFRACTION15{B|1041 - 1052}B1041 - 1052
16X-RAY DIFFRACTION16{B|1053 - 1061}B1053 - 1061
17X-RAY DIFFRACTION17{C|966 - 976}C966 - 976
18X-RAY DIFFRACTION18{C|977 - 987}C977 - 987
19X-RAY DIFFRACTION19{C|988 - 993}C988 - 993
20X-RAY DIFFRACTION20{C|994 - 1009}C994 - 1009
21X-RAY DIFFRACTION21{C|1010 - 1025}C1010 - 1025
22X-RAY DIFFRACTION22{C|1026 - 1044}C1026 - 1044
23X-RAY DIFFRACTION23{C|1045 - 1053}C1045 - 1053
24X-RAY DIFFRACTION24{C|1054 - 1061}C1054 - 1061
25X-RAY DIFFRACTION25{D|964 - 972}D964 - 972
26X-RAY DIFFRACTION26{D|973 - 987}D973 - 987
27X-RAY DIFFRACTION27{D|988 - 994}D988 - 994
28X-RAY DIFFRACTION28{D|995 - 1009}D995 - 1009
29X-RAY DIFFRACTION29{D|1010 - 1024}D1010 - 1024
30X-RAY DIFFRACTION30{D|1025 - 1034}D1025 - 1034
31X-RAY DIFFRACTION31{D|1035 - 1044}D1035 - 1044
32X-RAY DIFFRACTION32{D|1045 - 1054}D1045 - 1054
33X-RAY DIFFRACTION33{D|1055 - 1061}D1055 - 1061

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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