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- PDB-2w7r: Structure of the PDZ domain of Human Microtubule associated serin... -

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Basic information

Entry
Database: PDB / ID: 2w7r
TitleStructure of the PDZ domain of Human Microtubule associated serine- threonine kinase 4
ComponentsMICROTUBULE-ASSOCIATED SERINE/THREONINE-PROTEIN KINASE 4
KeywordsTRANSFERASE
Function / homology
Function and homology information


cytoskeleton organization / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / 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
PHOSPHATE ION / Microtubule-associated serine/threonine-protein kinase 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMuniz, J.R.C. / Elkins, J. / Wang, J. / Savitzky, P. / Roos, A. / Salah, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Muniz, J.R.C. / Elkins, J. / Wang, J. / Savitzky, P. / Roos, A. / Salah, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
CitationJournal: Protein Sci. / Year: 2010
Title: Unusual Binding Interactions in Pdz Domain Crystal Structures Help Explain Binding Mechanisms.
Authors: Elkins, J.M. / Gileadi, C. / Shrestha, L. / Phillips, C. / Wang, J. / Muniz, J.R.C. / Doyle, D.A.
History
DepositionDec 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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 4
B: MICROTUBULE-ASSOCIATED SERINE/THREONINE-PROTEIN KINASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3993
Polymers21,3042
Non-polymers951
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-12.1 kcal/mol
Surface area12830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.940, 100.940, 69.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.5157, -0.8555, -0.048), (-0.8489, 0.5177, -0.1064), (0.1158, -0.0141, -0.9932)
Vector: 0.9451, 2.7267, 32.0511)

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Components

#1: Protein MICROTUBULE-ASSOCIATED SERINE/THREONINE-PROTEIN KINASE 4


Mass: 10652.010 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 1143-1234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: O15021, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.06 Å3/Da / Density % sol: 40.38 % / Description: NONE
Crystal growDetails: 75MM NA PHOSPHATE, 91MM K PHOSPHATE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→29.14 Å / Num. obs: 32248 / % possible obs: 99.7 % / Observed criterion σ(I): 1.8 / Redundancy: 2.7 % / Biso Wilson estimate: 22.04 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.8
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.19 Å / SU ML: 0.24 / σ(F): 0.02 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1915 5.8 %
Rwork0.194 --
obs0.196 31282 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.11 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5078 Å20 Å20 Å2
2--2.5078 Å20 Å2
3----5.0156 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 5 139 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051508
X-RAY DIFFRACTIONf_angle_d0.8332073
X-RAY DIFFRACTIONf_dihedral_angle_d13.524507
X-RAY DIFFRACTIONf_chiral_restr0.05255
X-RAY DIFFRACTIONf_plane_restr0.004263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.37221180.29811959X-RAY DIFFRACTION83
1.64-1.68430.28751280.27032003X-RAY DIFFRACTION85
1.6843-1.73390.27191240.25112112X-RAY DIFFRACTION89
1.7339-1.78990.31591340.22392141X-RAY DIFFRACTION92
1.7899-1.85380.21311440.20472211X-RAY DIFFRACTION94
1.8538-1.9280.22891390.19542247X-RAY DIFFRACTION97
1.928-2.01570.23211400.18642325X-RAY DIFFRACTION98
2.0157-2.1220.22231440.18822328X-RAY DIFFRACTION99
2.122-2.25490.21681410.17652322X-RAY DIFFRACTION100
2.2549-2.42890.21411400.18882340X-RAY DIFFRACTION100
2.4289-2.67310.24121430.19852339X-RAY DIFFRACTION100
2.6731-3.05940.22341440.20532360X-RAY DIFFRACTION100
3.0594-3.85280.19461390.17312341X-RAY DIFFRACTION100
3.8528-27.19760.1871370.17542253X-RAY DIFFRACTION96
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)
12.49070.15870.0593-0.7180.22712.1218-0.1345-0.1135-0.48680.01410.0603-0.19460.3639-0.05480.07360.2510.03120.0360.10230.02690.187-19.911118.570614.8933
21.22060.012-0.88071.0875-0.84952.1309-0.120.01270.1691-0.11160.1654-0.13430.503-0.2708-0.03020.3215-0.06760.04480.1542-0.00010.2004-25.420219.80627.7091
30.877-0.32990.7721.1516-0.96471.1067-0.0538-0.084-0.3696-0.27060.1120.20710.3588-0.09470.03130.3352-0.03160.03880.1716-0.01560.2906-22.66215.98469.0718
4-0.70040.0344-0.03281.57020.21852.2026-0.0375-0.36360.0411-0.1621-0.0306-0.20330.02180.39280.06480.17140.0890.03390.25310.02630.1479-7.981528.740217.8129
5-1.26250.21730.20631.70990.27751.4192-0.0911-0.034-0.1726-0.10910.0917-0.3960.59050.41480.08230.25220.22080.1050.4190.02990.32982.38221.499514.1352
6-0.3907-0.2259-0.42921.35010.52813.3474-0.1032-0.23810.19020.090.0936-0.20780.01120.99630.08320.15950.0513-0.02220.46240.02020.2603-0.911931.256922.9971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 3:53)
2X-RAY DIFFRACTION2CHAIN A AND RESID 54:71)
3X-RAY DIFFRACTION3CHAIN A AND RESID 72:96)
4X-RAY DIFFRACTION4CHAIN B AND RESID 3:38)
5X-RAY DIFFRACTION5CHAIN B AND RESID 39:57)
6X-RAY DIFFRACTION6CHAIN B AND RESID 58:91)

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