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- PDB-3fz8: Crystal structure of glutamate decarboxylase beta from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 3fz8
TitleCrystal structure of glutamate decarboxylase beta from Escherichia coli: reduced Schiff base with PLP
ComponentsGlutamate decarboxylase beta
KeywordsLYASE / Glutamate decarboxylase / reduced form / Decarboxylase / Membrane / Pyridoxal phosphate
Function / homology
Function and homology information


glutamate decarboxylase / glutamate decarboxylase activity / glutamate catabolic process / intracellular pH elevation / pyridoxal phosphate binding / membrane / cytosol
Similarity search - Function
MYOD Basic-Helix-Loop-Helix Domain, subunit B - #50 / Aspartate Aminotransferase, domain 1 - #160 / Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 ...MYOD Basic-Helix-Loop-Helix Domain, subunit B - #50 / Aspartate Aminotransferase, domain 1 - #160 / Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Few Secondary Structures / Irregular / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PLR / Glutamate decarboxylase beta
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMalashkevich, V.N. / De Biase, D. / Bossa, F.
CitationJournal: to be published
Title: Crystal structure of glutamate decarboxylase beta from Escherichia coli: reduced Schiff base with PLP
Authors: Malashkevich, V.N. / De Biase, D. / Bossa, F.
History
DepositionJan 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate decarboxylase beta
B: Glutamate decarboxylase beta
C: Glutamate decarboxylase beta
D: Glutamate decarboxylase beta
E: Glutamate decarboxylase beta
F: Glutamate decarboxylase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,76712
Polymers316,3686
Non-polymers1,3996
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47410 Å2
ΔGint-217.3 kcal/mol
Surface area87500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.896, 116.894, 208.586
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -9999 - 9999 / Label seq-ID: -9999 - 9999

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Glutamate decarboxylase beta / GAD-beta


Mass: 52727.957 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b1493, gadB, JW1488 / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69910, glutamate decarboxylase
#2: Chemical
ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 2.0 M Ammonium sulfate, 0.1 M Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9791 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 1996
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 63606 / % possible obs: 95.41 %

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.88 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.853 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.139 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.861 / SU B: 40.481 / SU ML: 0.327 / SU R Cruickshank DPI: 0.325 / SU Rfree: 0.455 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3072 5.1 %RANDOM
Rwork0.165 ---
obs0.169 60684 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 12.472 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21835 0 90 60 21985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02222489
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.95630497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27152741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1723.9741092
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.143153718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.46315152
X-RAY DIFFRACTIONr_chiral_restr0.0990.23185
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117470
X-RAY DIFFRACTIONr_mcbond_it1.0021.513669
X-RAY DIFFRACTIONr_mcangle_it4.2352021950
X-RAY DIFFRACTIONr_scbond_it8.743208820
X-RAY DIFFRACTIONr_scangle_it3.2884.58547
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3631 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.295
BTIGHT POSITIONAL0.275
CTIGHT POSITIONAL0.295
DTIGHT POSITIONAL0.285
ETIGHT POSITIONAL0.45
FTIGHT POSITIONAL0.295
ATIGHT THERMAL3.2110
BTIGHT THERMAL2.9610
CTIGHT THERMAL3.1910
DTIGHT THERMAL3.0510
ETIGHT THERMAL3.4510
FTIGHT THERMAL2.9410
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 208 -
Rwork0.265 4273 -
all-4481 -
obs--96.3 %
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)
10.465-0.0296-0.12970.84140.19550.57240.01810.0117-0.0198-0.04010.0714-0.12750.08050.0995-0.08950.04430.0301-0.03230.0331-0.04040.055430.5409-17.9361-5.6904
20.73-0.05950.20610.4762-0.19690.64790.0553-0.0632-0.08440.1199-0.0029-0.05950.14120.0585-0.05240.12990.0181-0.05860.01590.00050.032612.6378-29.884612.7026
30.4416-0.13130.28720.66590.10880.7123-0.0067-0.0583-0.01120.03140.01860.04330.0128-0.1064-0.0120.0126-0.00850.00270.0240.00340.0035-24.8784-14.7485-12.6442
40.65310.2601-0.28930.50050.14820.50990.0438-0.04780.07760.0781-0.05320.1060.028-0.10030.00940.0148-0.00820.01720.0592-0.00810.0238-30.64734.4998.041
50.59970.18630.04220.5036-0.02620.50920.03030.0180.01-0.0231-0.03150.0278-0.07230.05440.00120.026-0.0054-0.00390.0087-0.00110.0025.371331.9418-7.8638
60.3234-0.1150.14930.70250.16920.62790.007-0.00710.0157-0.00640.037-0.0847-0.04020.052-0.0440.013-0.01130.00690.0114-0.00970.013220.895925.282514.6224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 466
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2B4 - 466
4X-RAY DIFFRACTION2B500
5X-RAY DIFFRACTION3C12 - 466
6X-RAY DIFFRACTION3C500
7X-RAY DIFFRACTION4D12 - 466
8X-RAY DIFFRACTION4D500
9X-RAY DIFFRACTION5E3 - 466
10X-RAY DIFFRACTION5E500
11X-RAY DIFFRACTION5E467 - 527
12X-RAY DIFFRACTION6F12 - 466
13X-RAY DIFFRACTION6F500

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