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- PDB-2dgk: Crystal structure of an N-terminal deletion mutant of Escherichia... -

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Basic information

Entry
Database: PDB / ID: 2dgk
TitleCrystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)
ComponentsGlutamate decarboxylase beta
KeywordsLYASE / GadB / GadBD1-14 / autoinhibition / substituted aldamine
Function / homology
Function and homology information


glutamate decarboxylase / glutamate decarboxylase activity / intracellular pH elevation / L-glutamate catabolic process / pyridoxal phosphate binding / membrane / cytosol
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #160 / Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / 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 ...Aspartate Aminotransferase, domain 1 - #160 / Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Glutamate decarboxylase beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Derived calculations / 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_ref_seq_dif / 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_ref_seq_dif.details / _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)308,95826
Polymers306,4026
Non-polymers2,55620
Water30,5351695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Glutamate decarboxylase beta
D: Glutamate decarboxylase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0079
Polymers102,1342
Non-polymers8737
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-82 kcal/mol
Surface area30570 Å2
MethodPISA
3
A: Glutamate decarboxylase beta
B: Glutamate decarboxylase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0079
Polymers102,1342
Non-polymers8737
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-78 kcal/mol
Surface area30540 Å2
MethodPISA
4
E: Glutamate decarboxylase beta
F: Glutamate decarboxylase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9458
Polymers102,1342
Non-polymers8116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-75 kcal/mol
Surface area30270 Å2
MethodPISA
5
D: Glutamate decarboxylase beta
E: Glutamate decarboxylase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9458
Polymers102,1342
Non-polymers8116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-38 kcal/mol
Surface area38890 Å2
MethodPISA
6
A: Glutamate decarboxylase beta
F: Glutamate decarboxylase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9458
Polymers102,1342
Non-polymers8116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-35 kcal/mol
Surface area39250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.770, 158.560, 201.420
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
Glutamate decarboxylase beta / GAD-beta / GadB


Mass: 51067.016 Da / Num. of mol.: 6 / Fragment: GadBD1-14 / Mutation: deletion of 14 N-terminal residues
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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1695 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22.5% PEG 2000 MME, 0.18M litium sulfate, 0.1M sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.954 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 2005 / 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: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 230800 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.068 / Net I/σ(I): 17.3
Reflection shellResolution: 1.9→2.2 Å / Redundancy: 7 % / Mean I/σ(I) obs: 8.7 / Num. unique all: 81214 / Rsym value: 0.217 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASERphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PMO

1pmo


Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2308 -RANDOM
Rwork0.218 ---
obs-230716 99 %-
Displacement parametersBiso mean: 28.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20922 0 152 1695 22769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.23
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.297 225 -
Rwork0.274 --
obs-22533 97.6 %

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