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- PDB-5cmc: Mnemiopsis leidyi ML032222a iGluR LBD E423S mutant glycine complex -

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Basic information

Entry
Database: PDB / ID: 5cmc
TitleMnemiopsis leidyi ML032222a iGluR LBD E423S mutant glycine complex
ComponentsML032222a iGluR
KeywordsMEMBRANE PROTEIN / Glutamate Receptor / Ion Channel
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / metal ion binding / membrane
Similarity search - Function
Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / ML032222a iGluR
Similarity search - Component
Biological speciesMnemiopsis leidyi (sea walnut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.28 Å
AuthorsMayer, M.L. / Thomas, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Molecular lock regulates binding of glycine to a primitive NMDA receptor.
Authors: Yu, A. / Alberstein, R. / Thomas, A. / Zimmet, A. / Grey, R. / Mayer, M.L. / Lau, A.Y.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Sep 27, 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_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ML032222a iGluR
B: ML032222a iGluR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1106
Polymers57,8392
Non-polymers2714
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-23 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.899, 123.138, 54.507
Angle α, β, γ (deg.)90.00, 111.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ML032222a iGluR


Mass: 28919.523 Da / Num. of mol.: 2 / Mutation: E423S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mnemiopsis leidyi (sea walnut) / Gene: ML032222a / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: A0A0R4I973*PLUS
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: Reservoir: 24% PEG 8K, 100 mM Cacodylate, 150 mM MgS04. Protein buffer: 150 mM NaCl, 10 mM HEPES, pH 7.0, 0.5 mM EDTA, 25 mM glycine
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→40 Å / Num. obs: 144111 / % possible obs: 96.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.92
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.5 / % possible all: 81.9

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4YKI

4yki


Resolution: 1.28→39.109 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.75 / Phase error: 14.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1568 13886 5.07 %Random selection
Rwork0.1343 ---
obs0.1355 273855 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→39.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 16 663 4679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0274353
X-RAY DIFFRACTIONf_angle_d1.2675882
X-RAY DIFFRACTIONf_dihedral_angle_d13.061609
X-RAY DIFFRACTIONf_chiral_restr0.074621
X-RAY DIFFRACTIONf_plane_restr0.007778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2802-1.29470.22113330.16525796X-RAY DIFFRACTION65
1.2947-1.310.16744070.15417438X-RAY DIFFRACTION83
1.31-1.3260.19154450.14678405X-RAY DIFFRACTION93
1.326-1.34270.1724490.13938449X-RAY DIFFRACTION94
1.3427-1.36040.17184580.14148575X-RAY DIFFRACTION94
1.3604-1.3790.16664610.13768586X-RAY DIFFRACTION96
1.379-1.39870.17534620.13578683X-RAY DIFFRACTION95
1.3987-1.41960.17784630.1338624X-RAY DIFFRACTION96
1.4196-1.44180.17884620.12578696X-RAY DIFFRACTION96
1.4418-1.46540.1614510.12298757X-RAY DIFFRACTION97
1.4654-1.49070.15194840.12018672X-RAY DIFFRACTION96
1.4907-1.51780.15924610.12038767X-RAY DIFFRACTION97
1.5178-1.5470.15124690.11938715X-RAY DIFFRACTION97
1.547-1.57860.15114930.11828822X-RAY DIFFRACTION97
1.5786-1.61290.15064450.11978824X-RAY DIFFRACTION98
1.6129-1.65040.15594750.11768759X-RAY DIFFRACTION97
1.6504-1.69170.14874890.11718901X-RAY DIFFRACTION98
1.6917-1.73750.17184650.13078817X-RAY DIFFRACTION98
1.7375-1.78860.17414580.13178862X-RAY DIFFRACTION98
1.7886-1.84630.15334930.13288959X-RAY DIFFRACTION99
1.8463-1.91230.15774800.1398949X-RAY DIFFRACTION99
1.9123-1.98890.15954510.13398993X-RAY DIFFRACTION99
1.9889-2.07940.15284740.12948962X-RAY DIFFRACTION99
2.0794-2.1890.15254370.1289085X-RAY DIFFRACTION99
2.189-2.32610.14024790.13238899X-RAY DIFFRACTION100
2.3261-2.50570.17784300.13819089X-RAY DIFFRACTION100
2.5057-2.75780.16794670.14159024X-RAY DIFFRACTION100
2.7578-3.15670.15074960.14519027X-RAY DIFFRACTION100
3.1567-3.97650.15424620.13499040X-RAY DIFFRACTION100
3.9765-39.12710.14635870.13858794X-RAY DIFFRACTION98

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