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- PDB-1m0q: Structure of Dialkylglycine Decarboxylase Complexed with S-1-amin... -

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Basic information

Entry
Database: PDB / ID: 1m0q
TitleStructure of Dialkylglycine Decarboxylase Complexed with S-1-aminoethanephosphonate
Components2,2-Dialkylglycine Decarboxylase
KeywordsLYASE / Decarboxylase / Pyridoxal phosphate
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-EPC / : / 2,2-dialkylglycine decarboxylase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsLiu, W. / Rogers, C.J. / Fisher, A.J. / Toney, M.D.
CitationJournal: Biochemistry / Year: 2002
Title: Aminophosphonate Inhibitors of Dialkylglycine Decarboxylase: Structural Basis for Slow Binding Inhibition
Authors: Liu, W. / Rogers, C.J. / Fisher, A.J. / Toney, M.D.
History
DepositionJun 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: 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_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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
Remark 999SEQUENCE AUTHORS STATE THAT RESIDUES GLN 15 AND GLY 81 FROM THE SWISSPROT ENTRY ARE INCORRECT. ...SEQUENCE AUTHORS STATE THAT RESIDUES GLN 15 AND GLY 81 FROM THE SWISSPROT ENTRY ARE INCORRECT. THESE RESIDUES SHOULD BE HIS 15 AND GLU 81 AS PRESENT IN AUTHORS' SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,2-Dialkylglycine Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9944
Polymers46,5771
Non-polymers4163
Water4,234235
1
A: 2,2-Dialkylglycine Decarboxylase
hetero molecules

A: 2,2-Dialkylglycine Decarboxylase
hetero molecules

A: 2,2-Dialkylglycine Decarboxylase
hetero molecules

A: 2,2-Dialkylglycine Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,97516
Polymers186,3104
Non-polymers1,66512
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
Unit cell
Length a, b, c (Å)150.810, 150.810, 85.050
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 2,2-Dialkylglycine Decarboxylase / DGD


Mass: 46577.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Plasmid: pBTac1 / Production host: Escherichia coli (E. coli)
References: UniProt: P16932, 2,2-dialkylglycine decarboxylase (pyruvate)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EPC / (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC ACID


Mass: 354.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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 Å3/Da / Density % sol: 61 %
Crystal growpH: 6.4
Details: 15% PEG 4000, 0.20 - 0.40 M SODIUM PYRUVATE, 0.015 M MES-KOH (pH 6.4)
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
25 mMpotassium phosphate1droppH7.5
30.020 mMPLP1drop
40.2 %(w/v)sodium azide1drop
515 %(w/v)PEG40001reservoir
615 mMMES- KOH1reservoirpH6.4
775-200 mMsodium pyruvate1reservoir
80.020 mMPLP1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 38642 / Num. obs: 38642 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -2 / Redundancy: 6.57 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.05 Å / % possible obs: 97.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 4.2 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Rmerge(I) obs: 0.407

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Processing

Software
NameClassification
TNTrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1DKA

1dka


Resolution: 2→20 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1932 5 %random
Rwork0.191 ---
obs0.194 38637 99.2 %-
Solvent computationBsol: 157 Å2 / ksol: 0.78 e/Å3
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 24 235 3511
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02633310.8
X-RAY DIFFRACTIONt_angle_deg1.86644931.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.2920100
X-RAY DIFFRACTIONt_trig_c_planes0.015732
X-RAY DIFFRACTIONt_gen_planes0.025245
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.194 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg1.98
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.290
X-RAY DIFFRACTIONt_planar_d0.0162
X-RAY DIFFRACTIONt_plane_restr0.025

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