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- PDB-2okk: The X-ray crystal structure of the 65kDa isoform of Glutamic Acid... -

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Entry
Database: PDB / ID: 2okk
TitleThe X-ray crystal structure of the 65kDa isoform of Glutamic Acid Decarboxylase (GAD65)
ComponentsGlutamate decarboxylase 2
KeywordsLYASE / PLP-dependent decarboxylase
Function / homologyPyridoxal-dependent decarboxylase conserved domain / Pyridoxal-phosphate binding site / Pyridoxal phosphate-dependent decarboxylase / MECP2 regulates transcription of genes involved in GABA signaling / GABA synthesis, release, reuptake and degradation / GABA synthesis / Pyridoxal phosphate-dependent transferase, major domain / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent transferase / glutamate decarboxylation to succinate ...Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal-phosphate binding site / Pyridoxal phosphate-dependent decarboxylase / MECP2 regulates transcription of genes involved in GABA signaling / GABA synthesis, release, reuptake and degradation / GABA synthesis / Pyridoxal phosphate-dependent transferase, major domain / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent transferase / glutamate decarboxylation to succinate / glutamate decarboxylase / glutamate decarboxylase activity / inhibitory synapse / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / neurotransmitter biosynthetic process / glutamate binding / anchored component of membrane / synaptic vesicle membrane / presynaptic membrane / chemical synaptic transmission / pyridoxal phosphate binding / cell junction / response to drug / Golgi membrane / axon / protein heterodimerization activity / perinuclear region of cytoplasm / plasma membrane / cytosol / Glutamate decarboxylase 2
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.3 Å resolution
AuthorsBuckle, A.M. / Fenalti, G. / Law, R.H.P. / Whisstock, J.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop.
Authors: Fenalti, G. / Law, R.H. / Buckle, A.M. / Langendorf, C. / Tuck, K. / Rosado, C.J. / Faux, N.G. / Mahmood, K. / Hampe, C.S. / Banga, J.P. / Wilce, M. / Schmidberger, J. / Rossjohn, J. / El-Kabbani, O. / Pike, R.N. / Smith, A.I. / Mackay, I.R. / Rowley, M.J. / Whisstock, J.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 17, 2007 / Release: Mar 27, 2007
RevisionDateData content typeGroupProviderType
1.0Mar 27, 2007Structure modelrepositoryInitial release
1.1Oct 16, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0814
Polyers56,7821
Non-polymers2983
Water1,65792
1
A: Glutamate decarboxylase 2
hetero molecules

A: Glutamate decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1618
Polyers113,5652
Non-polymers5976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area (Å2)13330
ΔGint (kcal/M)-110
Surface area (Å2)31890
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)78.251, 99.057, 120.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21
DetailsThe biological unit (dimer) is generated by applying crystallographic symmetry.

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Components

#1: Protein/peptide Glutamate decarboxylase 2 / / Glutamate decarboxylase 65 kDa isoform / GAD-65 / 65 kDa glutamic acid decarboxylase


Mass: 56782.328 Da / Num. of mol.: 1 / Fragment: residues 88-584 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Gene: GAD2, GAD65 / Plasmid name: pRJ / Genus (production host): Saccharomyces / Production host: Saccharomyces cerevisiae (baker's yeast) / Strain (production host): YRD-15 / References: UniProt: Q05329, glutamate decarboxylase
#2: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 2 / Formula: C4H9NO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3 / Glycerol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Formula: H2O / Water

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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: 2.05 / Density percent sol: 39.91 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% ethanol, 100 mM MES, 10 mM 2-mercaptoethanol, 20 mM CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 17-ID / Synchrotron site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Apr 1, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 / Relative weight: 1
ReflectionNumber: 78118 / Rmerge I obs: .059 / Highest resolution: 2.3 / Lowest resolution: 54.64 / Redundancy: 3.77 %
ReflectionD resolution high: 2.3 / D resolution low: 37.19 / Number obs: 20717
Reflection shell
Highest resolutionLowest resolutionNumber measured allNumber unique allDiffraction IDPercent possible all
2.302.42114422995198.85
2.422.57107362826199.19
2.572.75102622702199.08
2.752.9794682498199.56
2.973.2587742323199.44
3.253.6478362086199.17
3.644.2069391853198.97
4.205.1458911571198.85
5.147.2745231215197.96
7.2754.642247648191.86

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Phasing

Phasing MRD res high rotation: 2.5 / D res high translation: 2.5 / D res low rotation: 37.2 / D res low translation: 37.2

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Processing

Software
NameVersionClassificationContact authorContact author emailDateDescriptionLanguageLocationType
SCALACCP4_3.2.17 23/9/2005data scalingP.R. Evanspre[at]mrc-lmb.cam.ac.uk23/9/2005scale together multiple observations of reflectionsFortran_77http://www.ccp4.ac.uk/dist/html/INDEX.htmlother
ADSCQUANTUMdata collection
HKL-2000data reduction
CCP4(SCALA)data scaling
PHASERphasing
REFMAC5.2.0019refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OKJ
Correlation coeff Fo to Fc: 0.944 / Correlation coeff Fo to Fc free: 0.909 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 14.11 / Overall SU ML: 0.203 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.454 / Overall ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 / Solvent shrinkage radii: 0.8 / Solvent vdw probe radii: 1.4 / Solvent model details: BABINET MODEL WITH MASK
Displacement parametersB iso mean: 51.402 / Aniso B11: -1.32 / Aniso B12: 0 / Aniso B13: 0 / Aniso B22: 0.94 / Aniso B23: 0 / Aniso B33: 0.37
Least-squares processR factor R free: 0.256 / R factor R work: 0.196 / R factor obs: 0.2 / Highest resolution: 2.3 / Lowest resolution: 37.19 / Number reflection R free: 1077 / Number reflection obs: 20648 / Percent reflection R free: 5.2 / Percent reflection obs: 97.93
Refine hist #LASTHighest resolution: 2.3 / Lowest resolution: 37.19
Number of atoms included #LASTProtein: 3770 / Nucleic acid: 0 / Ligand: 20 / Solvent: 92 / Total: 3882
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223877
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9655246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995.000480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86824.038156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64015.000658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.40215.00016
X-RAY DIFFRACTIONr_chiral_restr0.1290.200578
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0202879
X-RAY DIFFRACTIONr_nbd_refined0.2030.2001811
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2002611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.200165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.200111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.20011
X-RAY DIFFRACTIONr_mcbond_it1.0212.0002463
X-RAY DIFFRACTIONr_mcangle_it1.9085.0003849
X-RAY DIFFRACTIONr_scbond_it3.7567.0001629
X-RAY DIFFRACTIONr_scangle_it5.20210.0001397
Refine LS shellHighest resolution: 2.3 / R factor R free: 0.354 / R factor R work: 0.247 / Lowest resolution: 2.36 / Number reflection R free: 66 / Number reflection R work: 1389 / Number reflection obs: 1455 / Total number of bins used: 20 / Percent reflection obs: 94.85

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