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- PDB-5dth: Crystal structure of MUPP1 PDZ8 domain from rattus norvegicus -

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Basic information

Entry
Database: PDB / ID: 5dth
TitleCrystal structure of MUPP1 PDZ8 domain from rattus norvegicus
ComponentsMultiple PDZ domain protein
KeywordsSIGNALING PROTEIN / CELL ADHESION / protein binding
Function / homology
Function and homology information


subapical complex / tight junction assembly / microtubule organizing center organization / Schmidt-Lanterman incisure / apicolateral plasma membrane / dendrite development / bicellular tight junction / endomembrane system / regulation of microtubule cytoskeleton organization / myelination ...subapical complex / tight junction assembly / microtubule organizing center organization / Schmidt-Lanterman incisure / apicolateral plasma membrane / dendrite development / bicellular tight junction / endomembrane system / regulation of microtubule cytoskeleton organization / myelination / intracellular protein transport / apical part of cell / cytoplasmic vesicle / postsynaptic density / cell adhesion / intracellular signal transduction / apical plasma membrane / synapse / glutamatergic synapse / dendrite / plasma membrane / cytoplasm
Similarity search - Function
Multiple PDZ domain protein / Unstructured region 10 on multiple PDZ protein / L27-2 / L27_2 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / PDZ domain / Pdz3 Domain ...Multiple PDZ domain protein / Unstructured region 10 on multiple PDZ protein / L27-2 / L27_2 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Multiple PDZ domain protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, J. / Lv, Y. / Zhu, H. / Liu, W.
CitationJournal: To Be Published
Title: Crystal structure and biochemical characteristics of MUPP1 PDZ8 domain from rattus norregicus
Authors: Lv, Y. / Li, J. / Zhu, H. / Liu, W.
History
DepositionSep 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_reflns_twin / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multiple PDZ domain protein
B: Multiple PDZ domain protein
C: Multiple PDZ domain protein
D: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)48,9314
Polymers48,9314
Non-polymers00
Water3,783210
1
A: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)12,2331
Polymers12,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)12,2331
Polymers12,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)12,2331
Polymers12,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Multiple PDZ domain protein


Theoretical massNumber of molelcules
Total (without water)12,2331
Polymers12,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.104, 39.242, 134.449
Angle α, β, γ (deg.)90.000, 92.730, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASPASPAA1314 - 14213 - 110
21GLUGLUASPASPBB1314 - 14213 - 110
12GLUGLUARGARGAA1314 - 14183 - 107
22GLUGLUARGARGCC1314 - 14183 - 107
13GLUGLUASNASNAA1314 - 14193 - 108
23GLUGLUASNASNDD1314 - 14193 - 108
14LYSLYSARGARGBB1313 - 14182 - 107
24LYSLYSARGARGCC1313 - 14182 - 107
15GLUGLUARGARGBB1314 - 14183 - 107
25GLUGLUARGARGDD1314 - 14183 - 107
16GLUGLUARGARGCC1314 - 14183 - 107
26GLUGLUARGARGDD1314 - 14183 - 107

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Multiple PDZ domain protein / Multi-PDZ domain protein 1


Mass: 12232.849 Da / Num. of mol.: 4 / Fragment: UNP residues 1312-1422
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mpdz, Mupp1 / Production host: Escherichia coli (E. coli) / References: UniProt: O55164
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NaI, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.896
11-h,-k,l20.104
ReflectionResolution: 1.95→50 Å / Num. obs: 31967 / % possible obs: 98.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.074 / Rrim(I) all: 0.13 / Χ2: 1.913 / Net I/av σ(I): 14.764 / Net I/σ(I): 8.2 / Num. measured all: 92533
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.982.90.66315430.580.4690.8161.46799.5
1.98-2.022.90.53516470.6480.3770.6581.55799.5
2.02-2.062.90.42515950.7480.2980.5211.56399.6
2.06-2.12.90.39515970.7870.2770.4841.62599.7
2.1-2.152.90.32415630.8130.2270.3981.6799.6
2.15-2.22.90.2916440.8730.2010.3541.63299.4
2.2-2.252.90.27815950.8680.1940.3411.70899.3
2.25-2.312.90.24916100.8970.1720.3041.63499.3
2.31-2.382.90.22615620.9190.1580.2771.78199.1
2.38-2.462.90.216340.9380.1380.2441.73498.9
2.46-2.542.90.18615790.940.1290.2281.80898.9
2.54-2.652.90.17315920.9520.1190.2112.05498.9
2.65-2.772.90.15316000.9580.1040.1852.13698.5
2.77-2.912.90.13216270.970.0910.1612.35398.5
2.91-3.12.90.10915910.980.0760.1332.50798.5
3.1-3.332.90.08416100.9860.0580.1032.44498.1
3.33-3.672.80.05815650.9930.040.0712.05697
3.67-4.22.80.04916000.9940.0340.062.1296.5
4.2-5.2930.04415920.9950.030.0542.03796.4
5.29-502.90.05216210.9950.0350.0632.40593.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DAZ

2daz


Resolution: 1.95→40.64 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.877 / SU B: 4.097 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 1614 5 %RANDOM
Rwork0.2247 ---
obs0.2266 30350 85.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.45 Å2 / Biso mean: 24.19 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-10.51 Å20 Å20.39 Å2
2---3.47 Å2-0 Å2
3----7.04 Å2
Refinement stepCycle: final / Resolution: 1.95→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 0 210 3391
Biso mean---29.23 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193259
X-RAY DIFFRACTIONr_bond_other_d0.0130.023097
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9554409
X-RAY DIFFRACTIONr_angle_other_deg2.21337069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86524.196143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60715539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0711523
X-RAY DIFFRACTIONr_chiral_restr0.120.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023815
X-RAY DIFFRACTIONr_gen_planes_other0.010.02762
X-RAY DIFFRACTIONr_mcbond_it2.4762.381718
X-RAY DIFFRACTIONr_mcbond_other2.4762.381717
X-RAY DIFFRACTIONr_mcangle_it3.4243.5552140
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110840.14
12B110840.14
21A97760.18
22C97760.18
31A99340.16
32D99340.16
41B97540.2
42C97540.2
51B102540.16
52D102540.16
61C97060.18
62D97060.18
LS refinement shellResolution: 1.95→1.98 Å

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