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- PDB-1dgd: AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRU... -

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Basic information

Entry
Database: PDB / ID: 1dgd
TitleAN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE
ComponentsDIALKYLGLYCINE DECARBOXYLASE
KeywordsLYASE
Function / homology
Function and homology information


2,2-dialkylglycine decarboxylase (pyruvate) / 2,2-dialkylglycine decarboxylase (pyruvate) activity / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small 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 / 2,2-dialkylglycine decarboxylase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsHohenester, E. / Jansonius, J.N.
Citation
Journal: Biochemistry / Year: 1994
Title: An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase.
Authors: Hohenester, E. / Keller, J.W. / Jansonius, J.N.
#1: Journal: Science / Year: 1993
Title: Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Sites
Authors: Toney, M.D. / Hohenester, E. / Jacob, S.W. / Jansonius, J.N.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Pseudomonas Cepacia 2,2-Dialkylglycine Decarboxylase. Sequence and Expression in Escherichia Coli of Structural and Repressor Genes
Authors: Keller, J.W. / Baurick, K.B. / Rutt, G.C. / O'Malley, M.V. / Sonafrank, N.L. / Reynolds, R. / Ebbesson, L.O. / Vajdos, F.F.
History
DepositionJun 29, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIALKYLGLYCINE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8465
Polymers46,3741
Non-polymers4724
Water1,78399
1
A: DIALKYLGLYCINE DECARBOXYLASE
hetero molecules

A: DIALKYLGLYCINE DECARBOXYLASE
hetero molecules

A: DIALKYLGLYCINE DECARBOXYLASE
hetero molecules

A: DIALKYLGLYCINE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,38620
Polymers185,4974
Non-polymers1,88916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)152.700, 152.700, 86.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Atom site foot note1: ATOMS WITH WEAK DENSITY HAVE BEEN REFINED WITH ZERO WEIGHT.
2: LYS 272 IS COVALENTLY BOUND TO THE COFACTOR PLP.
DetailsTHE MOLECULE IS A TETRAMER OF IDENTICAL SUBUNITS. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH COMPRISES ONE MONOMER. THE TETRAMER CAN BE GENERATED BY CRYSTALLOGRAPHIC DYADS. APPLYING THE FOLLOWING TRANSFORMATION TO THE COORDINATES IN THIS ENTRY WILL YIELD A DIMER: MTRIX1 1 -0.500000 0.866000 0.000000 0.00000 MTRIX2 1 0.866000 0.500000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 1.000000 28.87000 APPLYING THE FOLLOWING TRANSFORMATION TO THE DIMER WILL YIELD THE TETRAMER: MTRIX1 2 -1.000000 0.000000 0.000000 76.40000 MTRIX2 2 0.000000 -1.000000 0.000000 132.20000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DIALKYLGLYCINE DECARBOXYLASE


Mass: 46374.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria)
References: UniProt: P16932, 2,2-dialkylglycine decarboxylase (pyruvate)

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: DGDA_BURCE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 14 HIS 15 GLU 51 GLN 52 ILE 81 MET 82 VAL 82 LEU 83 ARG 307 PRO 308 PRO 309 LEU 309 GLY 312 ALA 312 THE PUBLISHED AMINO ACID SEQUENCE (REFERENCE 1) WAS CORRECTED AT THREE POSITIONS. RESEQUENCING OF SEVERAL GC-RICH REGIONS OF THE DGDA GENE VERIFIED THESE CHANGES (J.W. KELLER, PERSONAL COMMUNICATION): GLU 52 --> GLN 52 ILE 82, VAL 83 --> MET 82, LEU 83 ARG 308, CYS 309, PRO 310, PRO 311, ALA 312, GLY 313 --> PRO 308, LEU 309, PRO 310, ALA 311, ALA 312 (INCLUDES A DELETION). GLN 15 -->HIS 15 (M.D. TONEY ET AL., J. MOL. BIOL. 222: 873-875 (1991)).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 222.873-875 1991
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-60 mg/mlprotein1drop
25 mMpotassium phosphate1drop
30.015 mMPLP1drop
40.02 %(w/v)sodium azide1drop
515 %(w/v)PEG40001reservoir
615 mMmorpholinoethanesulfonic acid1reservoir
875-150 mMsodium pyruvate1reservoir
90.015 mMPLP1reservoir
7potassium hydroxide1reservoirto neutralize
100.02 %sodium azide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 14859 / % possible obs: 98.2 % / Num. measured all: 80899 / Rmerge(I) obs: 0.1

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.8→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.178 14224
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 29 99 3375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.009
X-RAY DIFFRACTIONt_it1.7
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d2.6
X-RAY DIFFRACTIONt_plane_restr0.009

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