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- PDB-2dgm: Crystal structure of Escherichia coli GadB in complex with iodide -

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Basic information

Entry
Database: PDB / ID: 2dgm
TitleCrystal structure of Escherichia coli GadB in complex with iodide
ComponentsGlutamate decarboxylase beta
KeywordsLYASE / GadB complexed with iodide
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
ACETIC ACID / FORMIC ACID / IODIDE ION / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Glutamate decarboxylase beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGruetter, M.G. / Capitani, G. / Gut, H.
Citation
Journal: Embo J. / Year: 2006
Title: Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB
Authors: Gut, H. / Pennacchietti, E. / John, R.A. / Bossa, F. / Capitani, G. / De Biase, D. / Gruetter, M.G.
#1: Journal: Embo J. / Year: 2003
Title: Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase
Authors: Capitani, G. / De Biase, D. / Aurizi, C. / Gut, H. / Bossa, F. / Gruetter, M.G.
History
DepositionMar 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)322,67659
Polymers316,3686
Non-polymers6,30853
Water34,6431923
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57140 Å2
ΔGint-209 kcal/mol
Surface area86370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.336, 91.804, 93.914
Angle α, β, γ (deg.)76.65, 76.94, 78.04
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glutamate decarboxylase beta / GAD-beta / GadB


Mass: 52727.957 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: gadB / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69910, glutamate decarboxylase

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Non-polymers , 6 types, 1976 molecules

#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1923 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.135M sodium acetate, 0.7M sodium formate, 13% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.3 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2003 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 191280 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.12 / Net I/σ(I): 5.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 17342 / Rsym value: 0.26 / % possible all: 84.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PMM

1pmm


Resolution: 1.95→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5338 -RANDOM
Rwork0.227 ---
obs-191251 92 %-
Displacement parametersBiso mean: 21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21578 0 172 1923 23673
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.26
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection% reflection
Rfree0.296 296 -
Rwork0.25 --
obs-16014 77 %

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