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- PDB-1dka: DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE ... -

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Basic information

Entry
Database: PDB / ID: 1dka
TitleDIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES
Components2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)2,2-dialkylglycine decarboxylase (pyruvate)
KeywordsLYASE(DECARBOXYLASE)
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: 2.6 Å
AuthorsToney, M.D. / Hohenester, E. / Jansonius, J.N.
Citation
Journal: Science / Year: 1993
Title: Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.
Authors: Toney, M.D. / Hohenester, E. / Cowan, S.W. / Jansonius, J.N.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Dialkylglycine Decarboxylase, a Decarboxylating Transaminase
Authors: Toney, M.D. / Keller, J.W. / Pauptit, R.A. / Jaeger, J. / Wise, M.K. / Sauder, U. / 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.A. / Ebbesson, L.O.E. / Vajdos, F.F.
History
DepositionJun 18, 1993Processing site: BNL
Revision 1.0Oct 15, 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: Derived calculations / Other
Category: pdbx_database_status / 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: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0825
Polymers46,5771
Non-polymers5044
Water2,612145
1
A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules

A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules

A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules

A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,32720
Polymers186,3104
Non-polymers2,01816
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: THE COFACTOR PYRIDOXAL-5'-PHOSPHATE (PLP 272) IS COVALENTLY ATTACHED TO LYS 272.
DetailsDIALKYLGLYCINE DECARBOXYLASE IS A TETRAMER OF IDENTICAL SUBUNITS. THE FOLLOWING TRANSFORMATIONS WILL GENERATE THE OTHER THREE SUBUNITS OF THE TETRAMER WHEN APPLIED TO THE COORDINATES PRESENTED IN THIS ENTRY: MTRIX1 1 -0.500000 0.866010 0.000000 0.00000 MTRIX2 1 0.866041 0.500000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 -1.000000 28.86753 MTRIX1 2 0.500000 -0.866010 0.000000 76.34753 MTRIX2 2 -0.866041 -0.500000 0.000000 132.24016 MTRIX3 2 0.000000 0.000000 -1.000000 28.86753 MTRIX1 3 -1.000000 0.000000 0.000000 76.34753 MTRIX2 3 0.000000 -1.000000 0.000000 132.24016 MTRIX3 3 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 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE) / 2,2-dialkylglycine decarboxylase (pyruvate)


Mass: 46577.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P16932, 2,2-dialkylglycine decarboxylase (pyruvate)

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Non-polymers , 5 types, 149 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#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.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY CYS 308 SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN ...SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY CYS 308 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 GLY 80 GLU 81 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) HAS BEEN CORRECTED (J.W. KELLER, PRIVATE COMMUNICATION). THE SEQUENCE PRESENTED IN THIS ENTRY IS THE CORRECTED SEQUENCE. THE FIRST TWO RESIDUES ARE NOT INCLUDED IN THE MODEL SINCE THEY ARE DISORDERED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Toney, M.D., (1991) J.Mol.Biol., 222, 873.
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 mMmorpholinoethanesulfonic acid1reservoir
615 %(w/v)PEG40001reservoir
7150 mMsodium pyruvate1reservoir
80.015 mMPLP1reservoir
9potassium hydroxide1reservoirto neutralize
100.02 %sodium azide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 16640 / % possible obs: 88 % / Rmerge(I) obs: 0.065

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.6→8 Å / Rfactor obs: 0.176
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 29 145 3426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.5
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_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.009

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