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- PDB-1us5: PUTATIVE GLUR0 LIGAND BINDING CORE WITH L-GLUTAMATE -

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Basic information

Entry
Database: PDB / ID: 1us5
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTahirov, T.H. / Inagaki, E.
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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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)33,6983
Polymers33,4891
Non-polymers2092
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.440, 69.476, 103.798
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: 33488.691 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.: 288 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5
Details: MICROBATCH METHOD UNDER OIL WAS USED. 20 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 22.5% PEG4000, 1M LITHIUM CHLORIDE AND 0.1M SODIUM CITRATE PH 5. THE CRYSTALLIZATION TEMPERATURE WAS 291 K. ...Details: MICROBATCH METHOD UNDER OIL WAS USED. 20 MG/ML OF PROTEIN SOLUTION WAS MIXED WITH 22.5% PEG4000, 1M LITHIUM CHLORIDE AND 0.1M SODIUM CITRATE PH 5. THE CRYSTALLIZATION TEMPERATURE WAS 291 K. THE CRYSTALS IN FORM OF PARALLELEPIPEDS WERE GROWN TO 0.03X0.03X0.15 MM WITHIN ONE MONTH. CRYOPROTECTANT CONTAINED 25% PEG4000, 18% ETHYLENE GLYCOL, 1M LITHIUM CHLORIDE AND 0.1M SODIUM CITRATE PH 5.
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: 1
DetectorType: RIGAKU IMAGE PLATE RAXIS-V / Detector: IMAGE PLATE / Date: Feb 15, 2003
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: 50003 / % possible obs: 97.7 % / Observed criterion σ(I): -0.5 / Redundancy: 4.32 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.1 / % possible all: 94.7
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Num. measured all: 215880 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 94.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1US4

1us4


Resolution: 1.5→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 814853.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2487 5 %RANDOM
Rwork0.184 ---
obs0.184 49845 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.25 Å2 / ksol: 0.51198 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 14 288 2539
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_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it3.612
X-RAY DIFFRACTIONc_scangle_it5.222.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 370 4.7 %
Rwork0.268 7568 -
obs--94.8 %
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
Highest resolution: 1.5 Å / Lowest resolution: 20 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
LS refinement shell
*PLUS
Highest resolution: 1.5 Å

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