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- PDB-2r4h: Crystal structure of a C1190S mutant of the 6th PDZ domain of hum... -

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Basic information

Entry
Database: PDB / ID: 2r4h
TitleCrystal structure of a C1190S mutant of the 6th 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 / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Cell junction / Nucleotide-binding / Phosphorylation / Tight junction
Function / homology
Function and homology information


positive regulation of cell-cell adhesion / endothelial cell morphogenesis / alpha-actinin binding / bicellular tight junction / cell periphery / cell projection / adherens junction / cell-cell junction / cell junction / protein-containing complex assembly ...positive regulation of cell-cell adhesion / endothelial cell morphogenesis / alpha-actinin binding / bicellular tight junction / cell periphery / cell projection / 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
HISTIDINE / 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: 2.05 Å
AuthorsUgochukwu, E. / Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Cooper, C. / Pike, A.C.W. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. ...Ugochukwu, E. / Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Cooper, C. / Pike, A.C.W. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of a C1190S mutant of the 6th PDZ domain of human membrane associated guanylate kinase.
Authors: Ugochukwu, E. / Pilka, E.S. / Hozjan, V. / Kavanagh, K.L. / Cooper, C. / Pike, A.C.W. / Elkins, J.M. / Doyle, D.A. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U.
History
DepositionAug 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,2698
Polymers38,4893
Non-polymers7815
Water2,054114
1
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1423
Polymers12,8301
Non-polymers3122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)12,8301
Polymers12,8301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2984
Polymers12,8301
Non-polymers4683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.052, 77.759, 50.182
Angle α, β, γ (deg.)90.00, 101.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 3 - 85 / Label seq-ID: 25 - 107

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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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: 12829.523 Da / Num. of mol.: 3 / Fragment: 6th PDZ domain: Residues 1149-1233 / Mutation: C1190S
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-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3350, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.006029 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006029 Å / Relative weight: 1
ReflectionResolution: 2.05→39.25 Å / Num. all: 17538 / Num. obs: 17538 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 9.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8383 / Rsym value: 0.683 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JIK

2jik


Resolution: 2.05→38.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.887 / SU B: 9.924 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25829 883 5.1 %RANDOM
Rwork0.18781 ---
all0.19148 16559 --
obs0.19148 16559 91.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.13 Å2
2---0.12 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 50 114 2255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.683
X-RAY DIFFRACTIONr_angle_other_deg1.228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.747
X-RAY DIFFRACTIONr_chiral_restr0.147
X-RAY DIFFRACTIONr_gen_planes_refined0.006
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_nbd_refined0.194
X-RAY DIFFRACTIONr_nbd_other0.196
X-RAY DIFFRACTIONr_nbtor_refined0.173
X-RAY DIFFRACTIONr_nbtor_other0.089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.131
X-RAY DIFFRACTIONr_mcbond_it5.197
X-RAY DIFFRACTIONr_mcbond_other2.263
X-RAY DIFFRACTIONr_mcangle_it5.773
X-RAY DIFFRACTIONr_scbond_it7.918
X-RAY DIFFRACTIONr_scangle_it10.191
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A478medium positional0.310.5
2B478medium positional0.20
3C478medium positional0.210
1A501loose positional0.865
2B501loose positional0.670.01
3C501loose positional0.80
1A478medium thermal1.672
2B478medium thermal1.60
3C478medium thermal1.430
1A501loose thermal1.4910
2B501loose thermal1.560.02
3C501loose thermal1.440
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 85 -
Rwork0.213 1233 -
obs--93.54 %
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)
10.94680.3441.3642.0702-1.03813.1742-0.20160.0622-0.05720.06950.0812-0.356-0.26860.12880.1203-0.03630-0.0091-0.0469-0.0259-0.065118.40675.02244.425
22.6022-0.2570.32551.8451-0.02720.91820.14330.1244-0.0056-0.2444-0.0758-0.0773-0.07010.1072-0.0675-0.03850.00970.0159-0.08520.0022-0.077410.680426.045613.692
31.57110.1610.22751.2463-0.40691.263-0.0122-0.06780.1252-0.03720.08130.0999-0.0502-0.0622-0.0691-0.03610.00440.0083-0.02950.0163-0.01673.180811.7758-17.5938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 8525 - 107
2X-RAY DIFFRACTION2BB3 - 8525 - 107
3X-RAY DIFFRACTION3CC3 - 8525 - 107

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