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- PDB-8wl1: The crystal structure of D-mandelate dehydrogenase from Lactobaci... -

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Basic information

Entry
Database: PDB / ID: 8wl1
TitleThe crystal structure of D-mandelate dehydrogenase from Lactobacillus brevis
Components2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / D-Mandelate dehydrogenase 2-Ketopantoate reductase Crystal structure
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: 1.75 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 crystal structure of D-mandelate dehydrogenase from Lactobacillus brevis
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


Theoretical massNumber of molelcules
Total (without water)33,3431
Polymers33,3431
Non-polymers00
Water2,450136
1
A: 2-dehydropantoate 2-reductase

A: 2-dehydropantoate 2-reductase


Theoretical massNumber of molelcules
Total (without water)66,6852
Polymers66,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area1850 Å2
ΔGint-18 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.310, 132.000, 59.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

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Components

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


Mass: 33342.637 Da / Num. of mol.: 1
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.: 136 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.3 M NaCl, 0.05M Tris pH 7.5, 30% Polyethylene glycol 335

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.75→34.92 Å / Num. obs: 32473 / % possible obs: 99.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 29.01 Å2 / CC1/2: 1 / Net I/σ(I): 29.5
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 32473 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→34.92 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.689 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 1647 5.1 %RANDOM
Rwork0.21636 ---
obs0.21818 30806 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.067 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.94 Å2
Refinement stepCycle: 1 / Resolution: 1.75→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 0 136 2459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192387
X-RAY DIFFRACTIONr_bond_other_d0.0010.022274
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9333267
X-RAY DIFFRACTIONr_angle_other_deg0.81235215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.95726.635104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45915378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.674153
X-RAY DIFFRACTIONr_chiral_restr0.0840.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
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_it2.2293.1691240
X-RAY DIFFRACTIONr_mcbond_other2.2293.1671239
X-RAY DIFFRACTIONr_mcangle_it3.0484.7361548
X-RAY DIFFRACTIONr_mcangle_other3.0474.7391549
X-RAY DIFFRACTIONr_scbond_it2.7333.4521147
X-RAY DIFFRACTIONr_scbond_other2.7323.4551148
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9955.0851717
X-RAY DIFFRACTIONr_long_range_B_refined5.20639.1782726
X-RAY DIFFRACTIONr_long_range_B_other5.16138.932680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 119 -
Rwork0.288 2162 -
obs--95.56 %

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