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- PDB-3ekm: Crystal structure of diaminopimelate epimerase form arabidopsis t... -

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Basic information

Entry
Database: PDB / ID: 3ekm
TitleCrystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP
ComponentsDiaminopimelate epimerase, chloroplastic
KeywordsISOMERASE / Diaminopimelate epimerase / Arabidopsis / PLP-independent amino acid racemase / aziridino-diaminopimelate / catalytic mechanism
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / chloroplast stroma / chloroplast
Similarity search - Function
Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID / Diaminopimelate epimerase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPillai, B. / Moorthie, V.A. / Cherney, M.M. / van Belkum, M.J. / Vederas, J.C. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis.
Authors: Pillai, B. / Moorthie, V.A. / van Belkum, M.J. / Marcus, S.L. / Cherney, M.M. / Diaper, C.M. / Vederas, J.C. / James, M.N.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Diaminopimelate epimerase, chloroplastic
B: Diaminopimelate epimerase, chloroplastic
C: Diaminopimelate epimerase, chloroplastic
D: Diaminopimelate epimerase, chloroplastic
E: Diaminopimelate epimerase, chloroplastic
F: Diaminopimelate epimerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,06612
Polymers205,8416
Non-polymers1,2256
Water21,8521213
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-54 kcal/mol
Surface area64070 Å2
MethodPISA
2
A: Diaminopimelate epimerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5112
Polymers34,3071
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Diaminopimelate epimerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5112
Polymers34,3071
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Diaminopimelate epimerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5112
Polymers34,3071
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Diaminopimelate epimerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5112
Polymers34,3071
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
E: Diaminopimelate epimerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5112
Polymers34,3071
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
F: Diaminopimelate epimerase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5112
Polymers34,3071
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.361, 136.606, 102.556
Angle α, β, γ (deg.)90.00, 119.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Diaminopimelate epimerase, chloroplastic / DAP epimerase


Mass: 34306.828 Da / Num. of mol.: 6 / Fragment: UNP residues 52-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: dapF / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) / References: UniProt: Q9LFG2, diaminopimelate epimerase
#2: Chemical
ChemComp-ZDR / (2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID


Mass: 204.224 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H16N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1213 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60%v/v Tacsimate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2006 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 108351 / Num. obs: 108351 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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Processing

Software
NameClassification
Blu-Icedata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GKE

2gke


Resolution: 2.3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5404 -random
Rwork0.187 ---
obs0.187 108351 99.9 %-
all-108351 --
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13222 0 84 1213 14519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.3→2.32 Å /
RfactorNum. reflection
Rfree0.294 94
Rwork0.261 -

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