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- PDB-1us4: PUTATIVE GLUR0 LIGAND BINDING CORE WITH L-GLUTAMATE -

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Basic information

Entry
Database: PDB / ID: 1us4
TitlePUTATIVE GLUR0 LIGAND BINDING CORE WITH L-GLUTAMATE
ComponentsPUTATIVE GLUR0 LIGAND BINDING CORE
KeywordsRECEPTOR / MEMBRANE PROTEIN / GLUTAMATE RECEPTOR / GLUR0 / L-GLUTAMATE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homologyTRAP transporter solute receptor, TAXI family / NMT1-like family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / GLUTAMIC ACID / Glutamate receptor
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsTahirov, T.H. / Inagaki, E. / Takahashi, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the Thermus Thermophilus Putative Periplasmic Glutamate/Glutamine-Binding Protein
Authors: Takahashi, H. / Inagaki, E. / Kuroishi, C. / Tahirov, T.H.
History
DepositionNov 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE GLUR0 LIGAND BINDING CORE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9323
Polymers33,7231
Non-polymers2092
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.518, 68.092, 81.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUTATIVE GLUR0 LIGAND BINDING CORE


Mass: 33723.168 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING CORE, RESIDUES 1-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83817*PLUS
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5
Details: VAPOUR DIFFUSION METHOD, 10 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION (20.3% PEG4000, 0.09M SODIUM CITRATE PH 5.0) AND EQUILIBRATED AGAINST RESERVOIR SOLUTION AT ROOM ...Details: VAPOUR DIFFUSION METHOD, 10 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH RESERVOIR SOLUTION (20.3% PEG4000, 0.09M SODIUM CITRATE PH 5.0) AND EQUILIBRATED AGAINST RESERVOIR SOLUTION AT ROOM TEMPERATURE (291 K). CRYSTALS IN FORM OF PARALLELEPIPEDS WERE GROWN TO 0.05X0.05X0.15 MM WITHIN 10 DAYS. CRYOPROTECTANT CONTENT: 25% PEG4000, 18% ETHYLENE GLYCOL AND 0.1M SODIUM CITRATE PH 5.0.
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220.3 %PEG40001reservoir
30.09 Msodium citrate1reservoirpH5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9, 0.9789, 0.9793
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97891
30.97931
ReflectionResolution: 1.75→50 Å / Num. obs: 28082 / % possible obs: 95.2 % / Observed criterion σ(I): -1 / Redundancy: 4.4 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 25.1
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 13.6 / % possible all: 98
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 50 Å / Num. measured all: 123941 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 13.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
ARP/wARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.75→28.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 823853.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FRIEDEL PAIRS WERE INCLUDED FOR THE REFINEMENT OF ANOMALOUS CONTRIBUTION OF SE ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2440 4.8 %RANDOM
Rwork0.178 ---
obs0.178 50956 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.815 Å2 / ksol: 0.343669 e/Å3
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2--0.28 Å20 Å2
3---1.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.75→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 14 235 2486
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it2.752
X-RAY DIFFRACTIONc_scbond_it3.532
X-RAY DIFFRACTIONc_scangle_it4.882.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.209 374 4.4 %
Rwork0.178 8040 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3EGL.PAREGL.TOP
Refinement
*PLUS
Lowest resolution: 29 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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