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- PDB-2q9v: Crystal structure of the C890S mutant of the 4th PDZ domain of hu... -

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Basic information

Entry
Database: PDB / ID: 2q9v
TitleCrystal structure of the C890S mutant of the 4th PDZ domain of human membrane associated guanylate kinase
ComponentsMembrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
KeywordsTRANSFERASE / PDZ / MEMBRANE ASSOCIATED GUANYLATE KINASE / CYS SER MUTANT / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / cell periphery / adherens junction / cell-cell junction / cell junction / protein-containing complex assembly / cell surface receptor signaling pathway ...positive regulation of cell-cell adhesion / alpha-actinin binding / bicellular tight junction / cell projection / cell periphery / adherens junction / cell-cell junction / cell junction / protein-containing complex assembly / cell surface receptor signaling pathway / cell adhesion / nucleolus / signal transduction / nucleoplasm / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Unstructured region on MAGI / Unstructured region on MAGI / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain ...Unstructured region on MAGI / Unstructured region on MAGI / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / PDZ domain / Domain with 2 conserved Trp (W) residues / Pdz3 Domain / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Papagrigoriou, E. / Cooper, C. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.A. ...Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Papagrigoriou, E. / Cooper, C. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.A. / Weigelt, J. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the C890S mutant of the 4th PDZ domain of human membrane associated guanylate kinase.
Authors: Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Papagrigoriou, E. / Cooper, C. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.A. / Weigelt, J. / Edwards, A. / Oppermann, U.
History
DepositionJun 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)9,8781
Polymers9,8781
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.821, 44.085, 54.512
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 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 / / BAI1-associated protein 1 / BAP-1 / Membrane-associated guanylate kinase inverted 1 / MAGI-1 / ...BAI1-associated protein 1 / BAP-1 / Membrane-associated guanylate kinase inverted 1 / MAGI-1 / Atrophin-1-interacting protein 3 / AIP3 / WW domain-containing protein 3 / WWP3 / Trinucleotide repeat-containing gene 19 protein


Mass: 9878.229 Da / Num. of mol.: 1 / Fragment: 4th PDZ Domain / Mutation: C890S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Brain / Gene: MAGI1, BAIAP1, BAP1, TNRC19 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q96QZ7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1:2 Protein:Well solution ratio, 20% PEG 3350, 10% Ethylene glycol, 200 mM Sodium acetate, 100 mM BTP pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 5, 2007 / Details: OSMIC
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→23 Å / Num. all: 5689 / Num. obs: 5434 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.069 / Rsym value: 0.075 / Net I/σ(I): 27.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.7 / Num. unique all: 759 / Rsym value: 0.313 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2I04,2PNT,2OPG
Resolution: 2→20.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.67 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23313 252 4.6 %RANDOM
Rwork0.16722 ---
obs0.17021 5230 96.24 %-
all-5434 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2→20.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms688 0 0 104 792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021700
X-RAY DIFFRACTIONr_bond_other_d0.0010.02474
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.959947
X-RAY DIFFRACTIONr_angle_other_deg0.83131152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.684589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9323.93933
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27615116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.89156
X-RAY DIFFRACTIONr_chiral_restr0.060.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02139
X-RAY DIFFRACTIONr_nbd_refined0.1810.2108
X-RAY DIFFRACTIONr_nbd_other0.170.2506
X-RAY DIFFRACTIONr_nbtor_refined0.160.2333
X-RAY DIFFRACTIONr_nbtor_other0.0750.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0840.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.233458
X-RAY DIFFRACTIONr_mcbond_other0.2663187
X-RAY DIFFRACTIONr_mcangle_it1.8625709
X-RAY DIFFRACTIONr_scbond_it3.2677272
X-RAY DIFFRACTIONr_scangle_it4.9511238
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 18 -
Rwork0.183 368 -
obs--94.84 %
Refinement TLS params.Method: refined / Origin x: -0.6197 Å / Origin y: 1.2253 Å / Origin z: -1.68 Å
111213212223313233
T-0.001 Å2-0.0044 Å20.0117 Å2-0.011 Å2-0.003 Å2--0.0029 Å2
L0.3978 °2-0.0382 °20.287 °2-1.1257 °20.0058 °2--0.5898 °2
S0.0178 Å °-0.0236 Å °-0.0367 Å °0.0065 Å °0.017 Å °-0.1164 Å °-0.0261 Å °0.0232 Å °-0.0348 Å °

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