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- PDB-5mz7: Crystal Structure of the third PDZ domain from the synaptic prote... -

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Basic information

Entry
Database: PDB / ID: 5mz7
TitleCrystal Structure of the third PDZ domain from the synaptic protein PSD-95 with incorporated Azidohomoalanine
ComponentsDisks large homolog 4
KeywordsPEPTIDE BINDING PROTEIN / Azidohomoalanine / Non-standard amino acid / unnatural amino acid / artificial amino acid / PSD-95
Function / homology
Function and homology information


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / LGI-ADAM interactions / proximal dendrite / neuron spine / Trafficking of AMPA receptors / protein localization to synapse / AMPA glutamate receptor clustering / cellular response to potassium ion / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of dendrite morphogenesis / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / dendritic spine organization / regulation of NMDA receptor activity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / NMDA selective glutamate receptor signaling pathway / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / kinesin binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / cell periphery / PDZ domain binding / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / neuromuscular junction / cerebral cortex development / cell-cell adhesion / kinase binding / cell junction / synaptic vesicle / cell-cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / 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
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsKudlinzki, D. / Lehner, F. / Witt, K. / Linhard, V.L. / Silvers, R. / Schwalbe, H.
CitationJournal: Chembiochem / Year: 2017
Title: Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding.
Authors: Lehner, F. / Kudlinzki, D. / Richter, C. / Muller-Werkmeister, H.M. / Eberl, K.B. / Bredenbeck, J. / Schwalbe, H. / Silvers, R.
History
DepositionJan 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2017Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.3Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 2.2Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 2.3Jan 17, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 4
B: Disks large homolog 4
C: Disks large homolog 4
D: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)43,2124
Polymers43,2124
Non-polymers00
Water10,034557
1
A: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)10,8031
Polymers10,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)10,8031
Polymers10,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)10,8031
Polymers10,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)10,8031
Polymers10,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.207, 34.078, 72.244
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Disks large homolog 4 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP90


Mass: 10802.950 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: P31016
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.1 M sodium citrate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.53→47.09 Å / Num. obs: 54545 / % possible obs: 97.6 % / Observed criterion σ(I): 2.1 / Redundancy: 2.3 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.7
Reflection shellResolution: 1.53→1.62 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.831 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFE

1bfe


Resolution: 1.53→47.086 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.23
RfactorNum. reflection% reflection
Rfree0.2206 2098 3.85 %
Rwork0.1836 --
obs0.1851 54518 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→47.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 0 557 3533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063095
X-RAY DIFFRACTIONf_angle_d0.7364178
X-RAY DIFFRACTIONf_dihedral_angle_d20.4461864
X-RAY DIFFRACTIONf_chiral_restr0.059451
X-RAY DIFFRACTIONf_plane_restr0.005576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5302-1.56580.33771330.28773335X-RAY DIFFRACTION94
1.5658-1.60490.32561380.27323453X-RAY DIFFRACTION98
1.6049-1.64830.28761390.25583475X-RAY DIFFRACTION98
1.6483-1.69680.30471390.24653471X-RAY DIFFRACTION98
1.6968-1.75160.28291390.23573457X-RAY DIFFRACTION98
1.7516-1.81420.27931400.21963531X-RAY DIFFRACTION98
1.8142-1.88680.24791390.20673478X-RAY DIFFRACTION98
1.8868-1.97270.24321400.19993492X-RAY DIFFRACTION98
1.9727-2.07670.23341400.18713502X-RAY DIFFRACTION98
2.0767-2.20680.22331410.17953509X-RAY DIFFRACTION98
2.2068-2.37720.2371400.1813492X-RAY DIFFRACTION98
2.3772-2.61640.25241420.18883542X-RAY DIFFRACTION98
2.6164-2.9950.24381410.18013525X-RAY DIFFRACTION98
2.995-3.77310.16471410.15473517X-RAY DIFFRACTION97
3.7731-47.10790.16351460.15263641X-RAY DIFFRACTION97

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