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- PDB-5ehs: Crystal structure of the Drosophila CG3822 KaiR1D ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 5ehs
TitleCrystal structure of the Drosophila CG3822 KaiR1D ligand binding domain complex with D-AP5
ComponentsRE06730p,GH17276
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of glutamate secretion, neurotransmission / regulation of synaptic activity / positive regulation of neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone / kainate selective glutamate receptor activity / calcium ion import across plasma membrane / presynaptic modulation of chemical synaptic transmission / synaptic transmission, glutamatergic ...positive regulation of glutamate secretion, neurotransmission / regulation of synaptic activity / positive regulation of neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone / kainate selective glutamate receptor activity / calcium ion import across plasma membrane / presynaptic modulation of chemical synaptic transmission / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane / postsynaptic membrane / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / 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. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / 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. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-phosphono-D-norvaline / 5-phosphono-L-norvaline / GH17276 / RE06730p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Drosophila grimshawi (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å
AuthorsDharkar, P. / Mayer, M.L.
CitationJournal: Neuron / Year: 2016
Title: Novel Functional Properties of Drosophila CNS Glutamate Receptors.
Authors: Li, Y. / Dharkar, P. / Han, T.H. / Serpe, M. / Lee, C.H. / Mayer, M.L.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RE06730p,GH17276
B: RE06730p,GH17276
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4616
Polymers59,6722
Non-polymers7894
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-6 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.700, 54.700, 147.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein RE06730p,GH17276


Mass: 29836.039 Da / Num. of mol.: 2
Fragment: unp residues 411-526; unp residues 650-794,unp residues 411-526; unp residues 650-794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Drosophila grimshawi (fry)
Gene: CG3822, Dgri\GH17276, Dgri_GH17276, GH17276 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q8MS48, UniProt: B4JUF1
#2: Chemical ChemComp-2JJ / 5-phosphono-D-norvaline


Type: D-peptide linking / Mass: 197.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO5P / Comment: antagonist*YM
#3: Chemical ChemComp-5OY / 5-phosphono-L-norvaline / (2~{S})-2-azanyl-5-phosphono-pentanoic acid


Mass: 197.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: Buffer 150 NaCl 10 HEPES pH 7.5 20 mM DL-AP5 2 mM EDTA Reservoir 19% PEG 1K 0.1 M Na Citrate pH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 97494 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 24.14
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 1.72 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1692: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EHM

5ehm


Resolution: 1.749→39.889 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 4580 4.7 %Random
Rwork0.1875 ---
obs0.1897 97494 97.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.749→39.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 48 326 4428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124229
X-RAY DIFFRACTIONf_angle_d1.135715
X-RAY DIFFRACTIONf_dihedral_angle_d12.5182553
X-RAY DIFFRACTIONf_chiral_restr0.059630
X-RAY DIFFRACTIONf_plane_restr0.008726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7494-1.76930.3436840.27252306X-RAY DIFFRACTION69
1.7693-1.79010.26021820.25272586X-RAY DIFFRACTION85
1.7901-1.81190.25031180.24952884X-RAY DIFFRACTION90
1.8119-1.83480.28981680.2392942X-RAY DIFFRACTION94
1.8348-1.8590.27711900.24823042X-RAY DIFFRACTION97
1.859-1.88440.28572020.23773124X-RAY DIFFRACTION99
1.8844-1.91140.27271200.23023142X-RAY DIFFRACTION100
1.9114-1.93990.31471480.22143228X-RAY DIFFRACTION100
1.9399-1.97020.26381280.22653226X-RAY DIFFRACTION100
1.9702-2.00250.2691840.22513116X-RAY DIFFRACTION100
2.0025-2.0370.26861280.21883188X-RAY DIFFRACTION100
2.037-2.07410.24441320.20433196X-RAY DIFFRACTION100
2.0741-2.1140.27151840.21763222X-RAY DIFFRACTION100
2.114-2.15710.29091840.20673076X-RAY DIFFRACTION100
2.1571-2.2040.20491480.20353248X-RAY DIFFRACTION100
2.204-2.25530.24451600.18483190X-RAY DIFFRACTION100
2.2553-2.31170.20931560.18813100X-RAY DIFFRACTION100
2.3117-2.37420.24871840.19193220X-RAY DIFFRACTION100
2.3742-2.4440.21721480.18913116X-RAY DIFFRACTION100
2.444-2.52290.24361720.19313148X-RAY DIFFRACTION100
2.5229-2.6130.2809960.19733276X-RAY DIFFRACTION100
2.613-2.71760.29181480.20153178X-RAY DIFFRACTION100
2.7176-2.84130.2971280.19873194X-RAY DIFFRACTION100
2.8413-2.9910.24191760.19623108X-RAY DIFFRACTION100
2.991-3.17840.24181760.19443168X-RAY DIFFRACTION100
3.1784-3.42370.25731160.18123272X-RAY DIFFRACTION100
3.4237-3.7680.22551780.16163044X-RAY DIFFRACTION99
3.768-4.31260.1571720.14293130X-RAY DIFFRACTION99
4.3126-5.43130.14961680.13013122X-RAY DIFFRACTION98
5.4313-39.89920.23011020.1693122X-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)
10.6369-0.0804-0.15611.10220.01650.63830.16260.08710.26290.4006-0.106-0.1295-0.3207-0.08110.00210.26950.01480.01260.03010.05910.198441.329741.311218.2128
20.9005-0.1909-0.25130.9864-0.00730.70870.0176-0.0020.086-0.02580.0651-0.1881-0.1035-0.1502-0.04970.19830.10220.01070.27410.02560.15154.66532.7536-5.1251
31.21190.26550.31421.125-0.13321.2790.06510.22960.06550.0369-0.16380.045-0.0885-0.21710.00040.13130.05730.0040.17570.01110.088133.396534.661911.9721
40.67390.05880.20170.6607-0.14420.6348-0.03030.1281-0.50820.1539-0.15130.20360.4132-0.0537-0.12360.2282-0.01410.104-0.0885-0.19310.332737.17027.65515.1575
50.32410.01380.21160.40880.19310.9088-0.06010.0595-0.019-0.1853-0.1110.20510.0326-0.2787-0.01520.20560.0545-0.07680.4197-0.26590.183428.503718.9414-7.6161
61.16890.2012-0.35090.86760.18431.2435-0.00710.1793-0.17110.1144-0.10890.03580.13480.10440.04630.14520.04710.01290.1494-0.02090.11446.768415.352412.3686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:113 )A5 - 113
2X-RAY DIFFRACTION2( CHAIN A AND RESID 114:221 )A114 - 221
3X-RAY DIFFRACTION3( CHAIN A AND RESID 222:264 )A222 - 264
4X-RAY DIFFRACTION4( CHAIN B AND RESID 5:111 )B5 - 111
5X-RAY DIFFRACTION5( CHAIN B AND RESID 112:223 )B112 - 223
6X-RAY DIFFRACTION6( CHAIN B AND RESID 224:262 )B224 - 262

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