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- PDB-8hpg: Crystal structure of phenylpyruvate reductase from Lactobacillus ... -

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Basic information

Entry
Database: PDB / ID: 8hpg
TitleCrystal structure of phenylpyruvate reductase from Lactobacillus sp. CGMCC 9967
ComponentsPhenylpyruvate reductase
KeywordsOXIDOREDUCTASE / phenylpyruvate reductase
Function / homologyphosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD binding / NAD(P)-binding domain superfamily / Phenylpyruvate reductase
Function and homology information
Biological speciesLactobacillus sp. CGMCC 9967 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.895 Å
AuthorsYang, J.H. / Song, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: One-Pot Biocatalytic Transformation of L-DOPA to D-Danshensu
Authors: Yang, J.H. / Song, W.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylpyruvate reductase
B: Phenylpyruvate reductase


Theoretical massNumber of molelcules
Total (without water)67,5052
Polymers67,5052
Non-polymers00
Water0
1
A: Phenylpyruvate reductase


Theoretical massNumber of molelcules
Total (without water)33,7531
Polymers33,7531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phenylpyruvate reductase


Theoretical massNumber of molelcules
Total (without water)33,7531
Polymers33,7531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.896, 48.970, 89.896
Angle α, β, γ (deg.)90.00, 116.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phenylpyruvate reductase


Mass: 33752.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. CGMCC 9967 (bacteria)
Gene: ppr / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M5IHP7

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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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 3.5
Details: PEG 1000, Citric acid, B-Nicotinamide adeinie dinucleotide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: May 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 3.89→23.49 Å / Num. obs: 3064 / % possible obs: 86.7394 % / Redundancy: 2 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.062 / Net I/σ(I): 7.29
Reflection shellResolution: 3.89→4.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.371 / Num. unique obs: 925 / CC1/2: 0.748 / % possible all: 54.7

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5refinement
HKL-2000data reduction
SHELXCDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.895→23.49 Å / Cor.coef. Fo:Fc: 0.664 / Cor.coef. Fo:Fc free: 0.605 / SU B: 8.898 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2795 141 4.6 %RANDOM
Rwork0.25755 ---
obs0.25875 2909 86.7394 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.129 Å2
Baniso -1Baniso -2Baniso -3
1--87.97 Å2-0 Å225.56 Å2
2--131.05 Å20 Å2
3----43.08 Å2
Refinement stepCycle: 1 / Resolution: 3.895→23.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 0 0 4680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134776
X-RAY DIFFRACTIONr_bond_other_d0.0040.0154637
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6356499
X-RAY DIFFRACTIONr_angle_other_deg1.0161.57610655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.645612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12322.613222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59915781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5921526
X-RAY DIFFRACTIONr_chiral_restr0.0460.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025414
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021042
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_it4.3514.62460
X-RAY DIFFRACTIONr_mcbond_other4.354.5992458
X-RAY DIFFRACTIONr_mcangle_it6.0936.8693068
X-RAY DIFFRACTIONr_mcangle_other6.0916.8683068
X-RAY DIFFRACTIONr_scbond_it3.2214.6322316
X-RAY DIFFRACTIONr_scbond_other3.2214.6322317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6496.9743432
X-RAY DIFFRACTIONr_long_range_B_refined7.97451.9095072
X-RAY DIFFRACTIONr_long_range_B_other7.97451.9125073
X-RAY DIFFRACTIONr_rigid_bond_restr1.97639413
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8966 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.895→3.895 Å
RfactorNum. reflection% reflection
Rfree0 20 -
Rwork0 6139 -
obs--21 %

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