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- PDB-6n2a: Meso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Iso... -

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Basic information

Entry
Database: PDB / ID: 6n2a
TitleMeso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Isoform 1)
ComponentsDiaminopimelate decarboxylase 1, chloroplastic
KeywordsLYASE / PLP / lysine / decarboxylase / meso-diaminopimelate
Function / homology
Function and homology information


diaminopimelate decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / chloroplast stroma / chloroplast / cytosol
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
LYSINE / PYRIDOXAL-5'-PHOSPHATE / Diaminopimelate decarboxylase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCrowther, J.M. / Dobson, R.C.J.
Funding support New Zealand, United States, 2items
OrganizationGrant numberCountry
Royal SocietyUOC1506 New Zealand
National Science Foundation (NSF, United States)MCB-1120541 United States
CitationJournal: To Be Published
Title: Active site gating provides stereochemical control for meso-diaminopimelate decarboxylase
Authors: Crowther, J.M. / Cross, P.J. / Oliver, M.R. / Leeman, M.M. / Bartl, A.J. / Weatherhead, A.W. / North, R.A. / Donovan, K.A. / Kessans, S.A. / Griffin, M.D.W. / Suzuki, H. / Hudson, A.O. / ...Authors: Crowther, J.M. / Cross, P.J. / Oliver, M.R. / Leeman, M.M. / Bartl, A.J. / Weatherhead, A.W. / North, R.A. / Donovan, K.A. / Kessans, S.A. / Griffin, M.D.W. / Suzuki, H. / Hudson, A.O. / Kassanmescheff, M. / Dobson, R.C.J.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diaminopimelate decarboxylase 1, chloroplastic
B: Diaminopimelate decarboxylase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6116
Polymers93,8232
Non-polymers7894
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-29 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.968, 88.624, 121.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-966-

HOH

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Components

#1: Protein Diaminopimelate decarboxylase 1, chloroplastic / DAPDC 1


Mass: 46911.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LYSA1, At3g14390, MLN21.17 / Plasmid: pET30a::At3g14390 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q949X7, diaminopimelate decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.22 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8 mg/ml protein in buffer containing 0.2 mM PLP and 0.4 mM lysine mixed in a 1:1 ratio with a reservoir solution consisting of 0.2 M magnesium chloride, 0.1 M Tris pH 7.5, 20%(w/v) PEG 6000.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.88→42.62 Å / Num. obs: 71841 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.058 / Rrim(I) all: 0.158 / Net I/σ(I): 9.6 / Num. measured all: 525698 / Scaling rejects: 179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.88-1.926.91.3013136245280.6780.5311.4071.598.7
9.01-42.626.50.02948747510.9990.0120.03127.599.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p3e

2p3e


Resolution: 1.88→42.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.937 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 2260 3.1 %RANDOM
Rwork0.1703 ---
obs0.1717 69528 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.38 Å2 / Biso mean: 24.775 Å2 / Biso min: 11.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.88→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 50 696 7197
Biso mean--18.01 35.01 -
Num. residues----833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136706
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176193
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.6389104
X-RAY DIFFRACTIONr_angle_other_deg1.3841.57314370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4995848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60222.759348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4281540
X-RAY DIFFRACTIONr_chiral_restr0.0770.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021373
LS refinement shellResolution: 1.88→1.928 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 163 -
Rwork0.294 5049 -
all-5212 -
obs--98.88 %

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