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- PDB-5h2y: Crystal structure of reduced DapF from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5h2y
TitleCrystal structure of reduced DapF from Corynebacterium glutamicum
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytosol
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
Diaminopimelate epimerase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Authors: Sagong, H.Y. / Kim, K.J.
History
DepositionOct 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopimelate epimerase
B: Diaminopimelate epimerase


Theoretical massNumber of molelcules
Total (without water)60,1092
Polymers60,1092
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.757, 118.938, 153.333
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Diaminopimelate epimerase / DAP epimerase


Mass: 30054.732 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: dapF, Cgl1943, cg2129 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NP73, diaminopimelate epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: Sodium phosphate monobasic, Potassium phosphate dibasic, CAPS, Lithium sulfate

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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: Jul 27, 2015
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→50 Å / Num. obs: 58955 / % possible obs: 96 % / Redundancy: 4.5 % / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.4 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
HKLdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.959 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 3114 5 %RANDOM
Rwork0.2071 ---
obs0.2094 58955 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.58 Å2 / Biso mean: 42.455 Å2 / Biso min: 18.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0 Å2
2---2.03 Å2-0 Å2
3---3.44 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 0 185 4273
Biso mean---44.68 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194158
X-RAY DIFFRACTIONr_bond_other_d0.0020.023905
X-RAY DIFFRACTIONr_angle_refined_deg2.181.9535661
X-RAY DIFFRACTIONr_angle_other_deg1.13338965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2235552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13824.59183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69415636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7751528
X-RAY DIFFRACTIONr_chiral_restr0.1250.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214844
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02906
X-RAY DIFFRACTIONr_mcbond_it4.3543.9772214
X-RAY DIFFRACTIONr_mcbond_other4.3543.9752213
X-RAY DIFFRACTIONr_mcangle_it6.1685.9482764
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 195 -
Rwork0.415 4180 -
all-4375 -
obs--95.32 %

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