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- PDB-5h2g: Crystal structure of oxidized DapF from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5h2g
TitleCrystal structure of oxidized 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 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,2984
Polymers60,1092
Non-polymers1882
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-18 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.738, 119.079, 155.585
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Ammonium sulfate, Bis-Tris

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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: Oct 20, 2014
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→94.56 Å / Num. obs: 59911 / % possible obs: 98.71 % / Redundancy: 8.1 % / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 5.1 / % possible all: 100

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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→94.56 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.135 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 3154 5 %RANDOM
Rwork0.1887 ---
obs0.1902 59911 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.62 Å2 / Biso mean: 36.193 Å2 / Biso min: 15.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å2-0 Å20 Å2
2---2.02 Å2-0 Å2
3---3.99 Å2
Refinement stepCycle: final / Resolution: 2→94.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 11 426 4563
Biso mean--37.89 45.77 -
Num. residues----558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194208
X-RAY DIFFRACTIONr_bond_other_d0.0020.023944
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9525727
X-RAY DIFFRACTIONr_angle_other_deg1.07339054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4845556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67824.516186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47815642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5811528
X-RAY DIFFRACTIONr_chiral_restr0.1360.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214890
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02922
X-RAY DIFFRACTIONr_mcbond_it3.7113.3432230
X-RAY DIFFRACTIONr_mcbond_other3.7043.3412229
X-RAY DIFFRACTIONr_mcangle_it4.7964.982784
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 252 -
Rwork0.228 4362 -
all-4614 -
obs--98.91 %

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