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- PDB-1d7v: CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYL... -

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Basic information

Entry
Database: PDB / ID: 1d7v
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH NMA
ComponentsPROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE))
KeywordsLYASE / ENZYME COMPLEXES / CATALYTIC MECHANISM / DECARBOXYLATION INHIBITOR
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
: / Chem-NMA / 2,2-dialkylglycine decarboxylase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMalashkevich, V.N. / Toney, M.D. / Strop, P. / Keller, J. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structures of dialkylglycine decarboxylase inhibitor complexes.
Authors: Malashkevich, V.N. / Strop, P. / Keller, J.W. / Jansonius, J.N. / Toney, M.D.
#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. / Vajdos, F.F.
History
DepositionOct 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,8924
Polymers46,4951
Non-polymers3963
Water64936
1
A: PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE))
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)187,56716
Polymers185,9814
Non-polymers1,58512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area28560 Å2
ΔGint-166 kcal/mol
Surface area51560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.200, 153.200, 86.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)) / DGD


Mass: 46495.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Plasmid: PKDHE19 / Production host: Escherichia coli (E. coli) / Strain (production host): TY103
References: UniProt: P16932, 2,2-dialkylglycine decarboxylase (pyruvate)
#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-NMA / N-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-2-METHYLALANINE / N-PYRIDOXYL-2-METHYLALANINE-5-PHOSPHATE


Mass: 334.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N2O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.16 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
131.5 mg/mlprotein1drop
25 mMpotassium phosphate1drop
30.015 mMPLP1drop
4150-200 mMsodium pyruvate1reservoir
515 %PEG40001reservoir
630 mM1reservoirKOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 6, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. obs: 14654 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 37.24 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / % possible all: 83.6
Reflection
*PLUS
Redundancy: 4.1 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DKB

2dkb


Resolution: 2.8→10 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.185 --
obs-14654 96 %
Rfree--96 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 164.5 Å2 / ksol: 0.67 e/Å3
Displacement parametersBiso mean: 41.82 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 24 36 3306
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.62
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.62
X-RAY DIFFRACTIONt_planar_d0.01

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