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- PDB-8wl3: The structure of D-mandelate dehydrogenase with L243W mutation -

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Basic information

Entry
Database: PDB / ID: 8wl3
TitleThe structure of D-mandelate dehydrogenase with L243W mutation
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / D-mandelate dehydrogenase
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytoplasm
Similarity search - Function
: / Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesLevilactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, F. / Rao, Z.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171471 China
CitationJournal: To Be Published
Title: The structure of D-mandelate dehydrogenase with L243W mutation
Authors: Liu, F. / Rao, Z.M.
History
DepositionSep 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydropantoate 2-reductase
B: 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)66,8312
Polymers66,8312
Non-polymers00
Water3,441191
1
A: 2-dehydropantoate 2-reductase

B: 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)66,8312
Polymers66,8312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544-x+1/2,y-1/2,-z-11
Buried area1940 Å2
ΔGint-18 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.540, 130.910, 58.090
Angle α, β, γ (deg.)90.00, 92.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-dehydropantoate 2-reductase / D-mandelate dehydrogenase / Ketopantoate reductase


Mass: 33415.688 Da / Num. of mol.: 2 / Mutation: L243W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Levilactobacillus brevis (bacteria) / Gene: CNR30_12720, UCCLB556_2064, LbMDH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A7Z6MKR0, 2-dehydropantoate 2-reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.6 M NaCl, 0.05M Tris pH 8.5, 30% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL17B / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→45.97 Å / Num. obs: 40808 / % possible obs: 94.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 16
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 40808 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.97 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.134 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25074 2117 5.2 %RANDOM
Rwork0.21313 ---
obs0.21508 38588 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.588 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.74 Å2
2---2.08 Å20 Å2
3---2.13 Å2
Refinement stepCycle: 1 / Resolution: 2→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 0 191 4883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194858
X-RAY DIFFRACTIONr_bond_other_d0.0010.024594
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9296663
X-RAY DIFFRACTIONr_angle_other_deg0.782310543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.83226.605215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.921156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021066
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6032.6642517
X-RAY DIFFRACTIONr_mcbond_other1.6022.6632516
X-RAY DIFFRACTIONr_mcangle_it2.4963.9853149
X-RAY DIFFRACTIONr_mcangle_other2.4953.9863150
X-RAY DIFFRACTIONr_scbond_it1.9472.9032339
X-RAY DIFFRACTIONr_scbond_other1.9472.9042340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1154.2713505
X-RAY DIFFRACTIONr_long_range_B_refined4.59832.435424
X-RAY DIFFRACTIONr_long_range_B_other4.55832.3495372
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9637 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 149 -
Rwork0.226 2437 -
obs--80.94 %

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