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- PDB-4yki: Mnemiopsis leidyi ML032222a iGluR LBD glycine complex -

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Basic information

Entry
Database: PDB / ID: 4yki
TitleMnemiopsis leidyi ML032222a iGluR LBD 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 / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsAlberstein, R.G. / Mayer, M.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes.
Authors: Alberstein, R. / Grey, R. / Zimmet, A. / Simmons, D.K. / Mayer, M.L.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 18, 2015Group: 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)58,1946
Polymers57,9232
Non-polymers2714
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-19 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.944, 123.388, 54.319
Angle α, β, γ (deg.)90.00, 111.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ML032222a iGluR


Mass: 28961.559 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Details: The construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain connected by a synthetic GT linker
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.: 817 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain ...The construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain connected by a synthetic GT linker

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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, hanging drop / pH: 6.5
Details: Reservoir: 18% PEG 8K, 100 mM Cacodylate, 150 mM MgS04. Protein buffer: 100 mM NaCl, 10 mM HEPES, pH 7.0, 0.5 mM EDTA, 2 mM Na glutamate, no added 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: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→40 Å / Num. obs: 169396 / % possible obs: 90.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.8
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2 / % possible all: 64.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S50

1s50


Resolution: 1.21→31.871 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.39 / Phase error: 16.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 14490 5.05 %Random selection
Rwork0.1335 ---
obs0.1349 144200 84.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.21→31.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 16 817 4839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084365
X-RAY DIFFRACTIONf_angle_d1.2185913
X-RAY DIFFRACTIONf_dihedral_angle_d12.7451629
X-RAY DIFFRACTIONf_chiral_restr0.072624
X-RAY DIFFRACTIONf_plane_restr0.006782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2104-1.22410.25181080.18662420X-RAY DIFFRACTION23
1.2241-1.23860.1692120.17513912X-RAY DIFFRACTION36
1.2386-1.25370.17692660.16865305X-RAY DIFFRACTION50
1.2537-1.26950.20263580.16346374X-RAY DIFFRACTION60
1.2695-1.28620.17924060.16687185X-RAY DIFFRACTION67
1.2862-1.30390.17554300.15647940X-RAY DIFFRACTION74
1.3039-1.32250.18464600.16158382X-RAY DIFFRACTION79
1.3225-1.34220.18674560.15498708X-RAY DIFFRACTION82
1.3422-1.36320.18814700.15158975X-RAY DIFFRACTION84
1.3632-1.38550.19325230.14249133X-RAY DIFFRACTION86
1.3855-1.40940.17174850.14359399X-RAY DIFFRACTION88
1.4094-1.43510.18055140.14239771X-RAY DIFFRACTION91
1.4351-1.46270.16075120.13359638X-RAY DIFFRACTION91
1.4627-1.49250.17675100.13449816X-RAY DIFFRACTION92
1.4925-1.5250.15215200.12859895X-RAY DIFFRACTION92
1.525-1.56040.17295320.124210006X-RAY DIFFRACTION94
1.5604-1.59950.1475530.124310058X-RAY DIFFRACTION94
1.5995-1.64270.17075170.120210131X-RAY DIFFRACTION95
1.6427-1.6910.16375520.126310165X-RAY DIFFRACTION95
1.691-1.74560.15075070.123410267X-RAY DIFFRACTION96
1.7456-1.8080.15555460.128210274X-RAY DIFFRACTION96
1.808-1.88040.14845540.128410379X-RAY DIFFRACTION97
1.8804-1.9660.15275360.127310379X-RAY DIFFRACTION97
1.966-2.06960.14575800.125510443X-RAY DIFFRACTION98
2.0696-2.19920.14365170.122910566X-RAY DIFFRACTION98
2.1992-2.3690.16215340.126210533X-RAY DIFFRACTION98
2.369-2.60730.17435060.137110600X-RAY DIFFRACTION99
2.6073-2.98430.17055870.141410548X-RAY DIFFRACTION99
2.9843-3.7590.15135730.133910624X-RAY DIFFRACTION99
3.759-31.88170.16356660.136310519X-RAY DIFFRACTION99

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