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- PDB-4zdm: Pleurobrachia bachei iGluR3 LBD Glycine Complex -

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Basic information

Entry
Database: PDB / ID: 4zdm
TitlePleurobrachia bachei iGluR3 LBD Glycine Complex
ComponentsGlutamate receptor kainate-like protein
KeywordsMEMBRANE PROTEIN / Glutamate Receptor / Ion Channel
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / signaling receptor activity / postsynaptic membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / 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 / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / Receptor, ligand binding region ...Ionotropic glutamate receptor, metazoa / 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 / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Glutamate receptor kainate-like protein
Similarity search - Component
Biological speciesPleurobrachia bachei (Pacific sea gooseberry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGrey, R.J. / 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
DepositionApr 17, 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_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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor kainate-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1496
Polymers28,8361
Non-polymers3135
Water7,314406
1
A: Glutamate receptor kainate-like protein
hetero molecules

A: Glutamate receptor kainate-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,29712
Polymers57,6712
Non-polymers62610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area2230 Å2
ΔGint-93 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.850, 159.850, 55.614
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-711-

HOH

DetailsThe dimer packing observed in this crystal form is not biologically relevant

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Components

#1: Protein Glutamate receptor kainate-like protein / PbiGluR3


Mass: 28835.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct contains residues N399-D519 and D660-N795 of the PbiGluR3 ligand binding domain connected by a synthetic GT linker, with an E399N mutation of the native sequence introduced to ...Details: The construct contains residues N399-D519 and D660-N795 of the PbiGluR3 ligand binding domain connected by a synthetic GT linker, with an E399N mutation of the native sequence introduced to facilitate removal of the affinity purification tag.
Source: (gene. exp.) Pleurobrachia bachei (Pacific sea gooseberry)
Gene: PbiGluR3 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: H6S0J1*PLUS
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Reservoir: 10% PEG 400, 1.6 M Li2SO4, 200 mM MgSO4, 100 mM cacodylate. Protein buffer: 100 mM NaCl, 10 mM HEPES, pH 7.5, 0.5 mM EDTA, 2 mM glutamate
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: RAYONIX MX300HS / Detector: CCD / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 67078 / % possible obs: 98.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 59.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.5 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YKI

4yki


Resolution: 1.5→29.384 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 3184 4.84 %Random
Rwork0.1564 ---
obs0.1574 65828 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→29.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 17 406 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152082
X-RAY DIFFRACTIONf_angle_d1.5672828
X-RAY DIFFRACTIONf_dihedral_angle_d12.897787
X-RAY DIFFRACTIONf_chiral_restr0.072306
X-RAY DIFFRACTIONf_plane_restr0.009380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52240.24391200.22612356X-RAY DIFFRACTION86
1.5224-1.54620.21731360.20442619X-RAY DIFFRACTION96
1.5462-1.57150.22261160.19772684X-RAY DIFFRACTION98
1.5715-1.59860.22611330.18252688X-RAY DIFFRACTION98
1.5986-1.62770.18371300.17582681X-RAY DIFFRACTION98
1.6277-1.6590.19391510.16382699X-RAY DIFFRACTION99
1.659-1.69290.1981240.15372686X-RAY DIFFRACTION97
1.6929-1.72970.20481350.16312682X-RAY DIFFRACTION99
1.7297-1.76990.19411370.15472723X-RAY DIFFRACTION99
1.7699-1.81420.1941530.1582686X-RAY DIFFRACTION98
1.8142-1.86320.171280.15432718X-RAY DIFFRACTION98
1.8632-1.9180.1741410.15162721X-RAY DIFFRACTION99
1.918-1.97990.15911520.14882722X-RAY DIFFRACTION99
1.9799-2.05070.15021360.14252737X-RAY DIFFRACTION99
2.0507-2.13270.15951410.13562740X-RAY DIFFRACTION99
2.1327-2.22980.16111350.13512756X-RAY DIFFRACTION99
2.2298-2.34730.14781270.13462768X-RAY DIFFRACTION100
2.3473-2.49430.1581510.14272769X-RAY DIFFRACTION100
2.4943-2.68680.15731310.14852804X-RAY DIFFRACTION100
2.6868-2.95690.18891420.15252798X-RAY DIFFRACTION100
2.9569-3.38420.17161500.17092822X-RAY DIFFRACTION100
3.3842-4.26170.17311640.14892847X-RAY DIFFRACTION100
4.2617-29.38920.1961510.17252938X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00390.00560.00060.0051-0.00080.004-0.046-0.05170.03150.02710.0073-0.0111-0.04210.0648-00.1575-0.0106-0.03970.1384-0.02420.135-69.608527.366524.5103
20.04160.0064-0.00980.0255-0.00930.046-0.0918-0.0821-0.150.00310.00840.04140.10780.0846-0.04440.12330.02360.00820.04460.01150.1358-65.950110.796110.0935
30.10950.0302-0.08370.0359-0.01880.0445-0.05890.0208-0.0909-0.01880.01120.0802-0.0152-0.047-0.03890.1040.0063-0.0330.0867-0.01560.0915-71.22218.78457.2624
40.02030.0099-0.00760.01230.00220.02150.01520.079-0.0428-0.0204-0.00270.0447-0.0545-0.06350.00630.08530.0078-0.0180.0633-0.0010.0604-71.069424.17772.8483
50.03390.059-0.03210.0713-0.01750.04160.0486-0.0085-0.0305-0.12560.0173-0.0411-0.0553-0.01240.00470.1410.0087-0.01910.068-0.01440.0791-59.998323.8349-1.9302
60.01330.00230.01620.02730.00860.0178-0.03710.0507-0.0365-0.3169-0.0789-0.00210.003-0.0458-0.09620.30220.0276-0.00690.1072-0.10140.0108-58.226617.3907-19.0787
70.22080.1151-0.04580.1296-0.0990.1563-0.09220.1758-0.0453-0.3174-0.11990.0275-0.06470.0178-0.08650.28110.0283-0.04470.0336-0.10090.0903-61.743716.5401-15.1019
80.02650.00730.01710.00230.00560.0209-0.0359-0.0185-0.0616-0.11560.0309-0.0478-0.00120.2367-0.01280.16010.03390.01680.1048-0.02190.1111-51.66416.543-8.3936
90.02850.01260.01230.0002-0.00990.0549-0.0247-0.02590.0008-0.0390.00510.0011-0.16320.03530.0020.10150.0057-0.03050.0756-0.00710.0734-64.028629.074211.2577
100.006-0.00370.00380.0146-0.00720.0090.0085-0.0779-0.0881-0.0056-0.0099-0.03730.09250.1836-0.00060.12030.0556-0.01550.15270.01240.1802-50.070215.04228.4859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:8)
2X-RAY DIFFRACTION2(chain A and resid 9:46)
3X-RAY DIFFRACTION3(chain A and resid 47:82)
4X-RAY DIFFRACTION4(chain A and resid 83:102)
5X-RAY DIFFRACTION5(chain A and resid 103:121)
6X-RAY DIFFRACTION6(chain A and resid 122:152)
7X-RAY DIFFRACTION7(chain A and resid 153:192)
8X-RAY DIFFRACTION8(chain A and resid 193:216)
9X-RAY DIFFRACTION9(chain A and resid 217:240)
10X-RAY DIFFRACTION10(chain A and resid 241:255)

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