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- PDB-8qzy: Structural and biochemical characterization of diaminopimelate ep... -

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Basic information

Entry
Database: PDB / ID: 8qzy
TitleStructural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / Pseudomonas aeruginosa / diaminopimelate epimerase / DapF / PA14_69690 / antimicrobials / lysine biosynthesis / peptidoglycan biosynthesis
Function / homologydiaminopimelate epimerase / Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / diaminopimelate epimerase activity / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / lysine biosynthetic process via diaminopimelate / cytoplasm / Diaminopimelate epimerase
Function and homology information
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsSchneider, P. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Structural and biochemical characterization of diaminopimelate epimerase from Pseudomonas aeruginosa
Authors: Schneider, P. / Blankenfeldt, W.
History
DepositionOct 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diaminopimelate epimerase
B: Diaminopimelate epimerase


Theoretical massNumber of molelcules
Total (without water)61,0082
Polymers61,0082
Non-polymers00
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-4 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.542, 88.580, 97.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diaminopimelate epimerase / DAP epimerase / PLP-independent amino acid racemase


Mass: 30503.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: dapF, PA14_69690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus / References: UniProt: Q02E84, diaminopimelate epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.49 M NaH2PO4, 0.91 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.69→65.45 Å / Num. obs: 61204 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.039 / Rrim(I) all: 0.139 / Χ2: 0.93 / Net I/av σ(I): 14.3 / Net I/σ(I): 14.3
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 8827 / CC1/2: 0.837 / Rpim(I) all: 0.433 / Rrim(I) all: 1.592 / Χ2: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→52.58 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 3085 5.05 %
Rwork0.1773 --
obs-61121 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.513 Å2
Refinement stepCycle: LAST / Resolution: 1.69→52.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4147 0 0 391 4538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124350
X-RAY DIFFRACTIONf_angle_d1.1435925
X-RAY DIFFRACTIONf_dihedral_angle_d6.099617
X-RAY DIFFRACTIONf_chiral_restr0.071650
X-RAY DIFFRACTIONf_plane_restr0.011799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.720.30231360.26552581X-RAY DIFFRACTION100
1.72-1.740.2541620.24212614X-RAY DIFFRACTION100
1.74-1.770.2641450.21812602X-RAY DIFFRACTION100
1.77-1.810.23291290.2122619X-RAY DIFFRACTION100
1.81-1.840.22761310.2052608X-RAY DIFFRACTION100
1.84-1.880.23251390.20292573X-RAY DIFFRACTION100
1.88-1.920.23341360.22619X-RAY DIFFRACTION100
1.92-1.960.23371560.19022599X-RAY DIFFRACTION100
1.96-2.010.21331320.17872635X-RAY DIFFRACTION100
2.01-2.070.20391410.1792601X-RAY DIFFRACTION100
2.07-2.130.23151210.18192638X-RAY DIFFRACTION100
2.13-2.20.23191610.17692585X-RAY DIFFRACTION100
2.2-2.280.23731490.17862624X-RAY DIFFRACTION100
2.28-2.370.21351300.16752635X-RAY DIFFRACTION100
2.37-2.480.21111210.17172669X-RAY DIFFRACTION100
2.48-2.610.20961320.17452653X-RAY DIFFRACTION100
2.61-2.770.22151410.18712634X-RAY DIFFRACTION100
2.77-2.980.24391510.19322642X-RAY DIFFRACTION100
2.98-3.280.19091390.1762675X-RAY DIFFRACTION100
3.28-3.760.19221350.16262686X-RAY DIFFRACTION100
3.76-4.730.19071470.14612708X-RAY DIFFRACTION100
4.73-52.580.23091510.18352836X-RAY DIFFRACTION100

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