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- PDB-3o46: Crystal structure of the PDZ domain of MPP7 -

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Basic information

Entry
Database: PDB / ID: 3o46
TitleCrystal structure of the PDZ domain of MPP7
ComponentsMAGUK p55 subfamily member 7
KeywordsPROTEIN BINDING / pdz domain / structural genomics consortium / SGC
Function / homology
Function and homology information


MPP7-DLG1-LIN7 complex / protein localization to adherens junction / bicellular tight junction assembly / establishment of cell polarity / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOG GTPase cycle / lateral plasma membrane / bicellular tight junction / RAC2 GTPase cycle ...MPP7-DLG1-LIN7 complex / protein localization to adherens junction / bicellular tight junction assembly / establishment of cell polarity / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOG GTPase cycle / lateral plasma membrane / bicellular tight junction / RAC2 GTPase cycle / RAC3 GTPase cycle / signaling adaptor activity / RAC1 GTPase cycle / positive regulation of protein-containing complex assembly / adherens junction / cell-cell junction / cell junction / cell cortex / molecular adaptor activity / cadherin binding / protein domain specific binding / nucleoplasm / plasma membrane
Similarity search - Function
MPP7, SH3 domain / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...MPP7, SH3 domain / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MAGUK p55 subfamily member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsNedyalkova, L. / Tong, Y. / Tempel, W. / Zhong, N. / Guan, X. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Nedyalkova, L. / Tong, Y. / Tempel, W. / Zhong, N. / Guan, X. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the PDZ domain of MPP7
Authors: Nedyalkova, L. / Tong, Y. / Tempel, W. / Zhong, N. / Guan, X. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAGUK p55 subfamily member 7


Theoretical massNumber of molelcules
Total (without water)10,10214
Polymers10,1021
Non-polymers013
Water1,24369
1
A: MAGUK p55 subfamily member 7

A: MAGUK p55 subfamily member 7

A: MAGUK p55 subfamily member 7


Theoretical massNumber of molelcules
Total (without water)30,30742
Polymers30,3073
Non-polymers039
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4210 Å2
ΔGint-16 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.616, 66.616, 46.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-33-

HOH

21A-49-

HOH

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Components

#1: Protein MAGUK p55 subfamily member 7


Mass: 10102.445 Da / Num. of mol.: 1 / Fragment: PDZ Domain (UNP residues 135-225)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPP7 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q5T2T1
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
21001
11001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97904
ROTATING ANODERIGAKU FR-E DW21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 17, 2010
RIGAKU RAXIS2IMAGE PLATEJun 13, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2SINGLE WAVELENGTHMx-ray1
1SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
21.54181
ReflectionResolution: 1.3→40 Å / Num. obs: 28982 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.041 / Χ2: 1.566 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.325.50.75128471.66100
1.32-1.355.50.66328151.59999.8
1.35-1.375.50.52228821.6199.9
1.37-1.45.50.42128441.514100
1.4-1.435.50.36928211.49199.9
1.43-1.465.60.3228501.45399.9
1.46-1.55.60.23128991.4199.9
1.5-1.545.60.18928121.43100
1.54-1.595.60.15928521.419100
1.59-1.645.60.12828011.389100
1.64-1.75.60.10129041.441100
1.7-1.765.60.08428371.409100
1.76-1.845.70.06828771.459100
1.84-1.945.70.05428351.587100
1.94-2.065.70.05328092.031100
2.06-2.225.60.04928852.329100
2.22-2.455.60.0428491.918100
2.45-2.85.50.0328651.429100
2.8-3.535.80.02728371.419100
3.53-405.50.02528001.30897.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→33.308 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.192 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 1.195 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY . The structure was originally solved using data measured with the same crystal on a copper rotating anode. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY . The structure was originally solved using data measured with the same crystal on a copper rotating anode. The model was refined against higher resolution synchrotron data. Scaled synchrotron intensities have been deposited along with the structure factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 1449 5.009 %RANDOM
Rwork0.1839 ---
obs0.184 28929 99.807 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 44.67 Å2 / Biso mean: 12.991 Å2 / Biso min: 9.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.584 Å20.292 Å20 Å2
2--0.584 Å20 Å2
3----0.876 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms617 0 13 69 699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022700
X-RAY DIFFRACTIONr_bond_other_d0.0020.02493
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.987963
X-RAY DIFFRACTIONr_angle_other_deg0.92131231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1652526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.915140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.682155
X-RAY DIFFRACTIONr_chiral_restr0.110.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02121
X-RAY DIFFRACTIONr_mcbond_it1.9021.5453
X-RAY DIFFRACTIONr_mcbond_other0.5651.5185
X-RAY DIFFRACTIONr_mcangle_it2.9732749
X-RAY DIFFRACTIONr_scbond_it3.9893247
X-RAY DIFFRACTIONr_scangle_it6.0284.5203
X-RAY DIFFRACTIONr_rigid_bond_restr1.41331193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3340.2381140.2172020213799.86
1.334-1.370.2211030.19619722075100
1.37-1.410.1641310.1691877201299.801
1.41-1.4530.21960.1661866196499.898
1.453-1.5010.1651130.1451785190099.895
1.501-1.5530.185840.1521745183299.836
1.553-1.6120.207840.1551689177499.944
1.612-1.6770.151760.1531647172599.884
1.677-1.7520.188750.1581565164199.939
1.752-1.8370.168730.1591496157199.873
1.837-1.9360.206740.1571421149799.866
1.936-2.0530.187600.1551337139999.857
2.053-2.1940.156840.1551257134299.925
2.194-2.3690.122470.1511991246100
2.369-2.5940.203550.1871093115199.739
2.594-2.8980.187370.21007104599.904
2.898-3.3420.192530.215856909100
3.342-4.0830.199340.195752786100
4.083-5.7310.206350.19658161999.515
5.731-33.3080.31210.32431536093.333

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