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- PDB-3bpu: Crystal structure of the 3rd PDZ domain of human membrane associa... -

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Basic information

Entry
Database: PDB / ID: 3bpu
TitleCrystal structure of the 3rd PDZ domain of human membrane associated guanylate kinase, C677S and C709S double mutant
ComponentsMembrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
KeywordsTRANSFERASE / PDZ / MEMBRANE ASSOCIATED GUANYLATE KINASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-binding / Cell junction / Nucleotide-binding / Phosphoprotein / Tight junction
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. / PDZ domain / Pdz3 Domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPilka, E.S. / Hozjan, V. / Cooper, C. / Pike, A.C.W. / Elkins, J. / Doyle, D.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Pilka, E.S. / Hozjan, V. / Cooper, C. / Pike, A.C.W. / Elkins, J. / Doyle, D.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the 3rd PDZ domain of human membrane associated guanylate kinase, C677S and C709S double mutant.
Authors: Pilka, E.S. / Hozjan, V. / Cooper, C. / Pike, A.C.W. / Elkins, J. / Doyle, D.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Oppermann, U.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6813
Polymers9,5501
Non-polymers1312
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.472, 61.578, 80.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-902-

ZN

21A-15-

HOH

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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: 9550.030 Da / Num. of mol.: 1 / Fragment: 3rd PDZ domain: Residues 640-721 / Mutation: C677S, C709S
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): BL21(DE3)-R3-pRARE2 / References: UniProt: Q96QZ7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.05M Zn acetate pH 6.2, 30% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97912 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2007
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.6→40.06 Å / Num. all: 10994 / Num. obs: 10446 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.074 / Rsym value: 0.03 / Net I/σ(I): 17.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1571 / Rsym value: 0.346 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1UJV, 1G9O

1ujv

1g9o


Resolution: 1.6→28.74 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.335 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25112 515 4.7 %RANDOM
Rwork0.20202 ---
obs0.20418 10446 99.96 %-
all-10446 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.883 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2---0.12 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms630 0 2 72 704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022641
X-RAY DIFFRACTIONr_bond_other_d0.0020.02420
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.975865
X-RAY DIFFRACTIONr_angle_other_deg0.91631043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.983584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.3892625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72315116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.265153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02107
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5923423
X-RAY DIFFRACTIONr_mcbond_other1.0843178
X-RAY DIFFRACTIONr_mcangle_it4.8625680
X-RAY DIFFRACTIONr_scbond_it6.9538218
X-RAY DIFFRACTIONr_scangle_it8.17811185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 43 -
Rwork0.296 753 -
obs--100 %
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)
110.0599-7.68871.73969.0591-1.23922.43420.04770.59040.50580.0334-0.2552-0.3474-0.38680.14130.20750.0749-0.04410.00680.1190.02740.0747-6.542811.8708-18.1926
23.6776-4.2509-2.98085.1342.15210.0068-0.4186-0.0760.16930.06450.233-0.2096-0.44370.80750.18560.073-0.048-0.14940.0820.01680.0161-0.75933.8055-5.1144
37.51570.58670.13218.91240.01494.32180.40380.1469-0.05531.4289-0.2165-0.3523-0.33060.2911-0.18720.3334-0.033-0.075-0.00390.0024-0.0522-9.387212.3012-5.6034
42.75440.63120.99116.38261.70933.9391-0.0234-0.00410.03250.1250.1256-0.4539-0.18210.273-0.10220.033-0.0077-0.00340.12230.00290.0707-8.927310.1601-13.3678
51.3416-0.25240.01170.9555-0.99943.1776-0.02980.05820.04290.04970.031-0.10990.00020.12-0.00120.0548-0.0047-0.00390.0934-0.00140.0532-10.81585.4284-10.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA638 - 6471 - 10
2X-RAY DIFFRACTION2AA648 - 65611 - 19
3X-RAY DIFFRACTION3AA657 - 67720 - 40
4X-RAY DIFFRACTION4AA678 - 69141 - 54
5X-RAY DIFFRACTION5AA692 - 72555 - 88

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