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- PDB-5x7m: Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) f... -

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Basic information

Entry
Database: PDB / ID: 5x7m
TitleCrystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum
ComponentsDiaminopimelate decarboxylase
KeywordsLYASE / Decarboxylase
Function / homology
Function and homology information


diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / pyridoxal phosphate binding
Similarity search - Function
Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain ...Diaminopimelate decarboxylase, LysA / Orn/DAP/Arg decarboxylase 2, conserved site / Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site / Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. / Orn/DAP/Arg decarboxylases family 2 signature 2. / Orn/DAP/Arg decarboxylase 2, C-terminal / Pyridoxal-dependent decarboxylase, C-terminal sheet domain / Ornithine/DAP/Arg decarboxylase / Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Diaminopimelate decarboxylase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSon, H.-F. / Kim, K.-J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum.
Authors: Son, H.F. / Kim, K.J.
History
DepositionFeb 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diaminopimelate decarboxylase
B: Diaminopimelate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5504
Polymers97,0562
Non-polymers4942
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-16 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.650, 92.013, 94.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Diaminopimelate decarboxylase / / DAPDC


Mass: 48528.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: lysA, Cgl1180, cg1334 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-T1R / References: UniProt: P09890, diaminopimelate decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate tribasic, Sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2016
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→94.76 Å / Num. obs: 36222 / % possible obs: 96 % / Redundancy: 4.7 % / Net I/σ(I): 26.88
Reflection shellResolution: 2.4→2.44 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKV

1hkv


Resolution: 2.4→23.708 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.747 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1898 5 %RANDOM
Rwork0.1864 ---
obs0.1897 36222 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.41 Å2 / Biso mean: 35.912 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å20 Å2
2--0.76 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.4→23.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 30 131 6813
Biso mean--51 34.55 -
Num. residues----886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196808
X-RAY DIFFRACTIONr_bond_other_d0.0020.026380
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9629260
X-RAY DIFFRACTIONr_angle_other_deg1.025314642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5845884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49924.156308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.097151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0331546
X-RAY DIFFRACTIONr_chiral_restr0.0950.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027884
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021522
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 110 -
Rwork0.289 2347 -
all-2457 -
obs--84.78 %

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