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- PDB-7yb2: Crystal Structure of anthrol reductase (CbAR) in complex with NAD... -

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Basic information

Entry
Database: PDB / ID: 7yb2
TitleCrystal Structure of anthrol reductase (CbAR) in complex with NADP+ and emodin
ComponentsVersicolorin reductase
KeywordsOXIDOREDUCTASE / anthrol reductase / chiral alcohol / emodin
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Versicolorin reductase
Similarity search - Component
Biological speciesCercospora sp. JNU001 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHou, X.D. / Rao, Y.J.
Funding support China, 4items
OrganizationGrant numberCountry
Other private2021YFC2102700 China
Other privateBK20202002 China
Other privateKYCX20_1812 China
Other privateKYCX20_1816 China
CitationJournal: Nat Commun / Year: 2023
Title: Structural analysis of an anthrol reductase inspires enantioselective synthesis of enantiopure hydroxycycloketones and beta-halohydrins.
Authors: Hou, X. / Xu, H. / Yuan, Z. / Deng, Z. / Fu, K. / Gao, Y. / Liu, C. / Zhang, Y. / Rao, Y.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Versicolorin reductase
B: Versicolorin reductase
C: Versicolorin reductase
D: Versicolorin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,88716
Polymers120,4644
Non-polymers4,42312
Water10,251569
1
B: Versicolorin reductase
C: Versicolorin reductase
D: Versicolorin reductase
hetero molecules

A: Versicolorin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,88716
Polymers120,4644
Non-polymers4,42312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-x,-y+1/2,z-1/21
Buried area14250 Å2
ΔGint-87 kcal/mol
Surface area35500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.797, 123.362, 126.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Versicolorin reductase


Mass: 30115.912 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora sp. JNU001 (fungus) / Gene: CB0940_02504 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G5I2X5
#2: Chemical
ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN


Mass: 270.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 15% isopropanol and 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 89048 / % possible obs: 99.1 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.999 / Χ2: 0.023 / Net I/σ(I): 8.3 / Num. measured all: 1074411
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.85-1.887.10.56939680.865190.3
1.88-1.927.90.48541780.863194.3
1.92-1.958.90.43343560.895197.8
1.95-1.9910.60.37244050.918199.8
1.99-2.0412.60.32544750.951199.9
2.04-2.0813.20.27644281.0121100
2.08-2.1413.10.22944731.021100
2.14-2.1912.90.20244491.0441100
2.19-2.2612.70.1844231.0541100
2.26-2.33120.15744951.0591100
2.33-2.41130.13644351.0761100
2.41-2.5113.30.12544781.049199.9
2.51-2.6313.10.1144701.0171100
2.63-2.7612.60.09344791.0011100
2.76-2.9412.40.0845150.9641100
2.94-3.1613.50.07145050.9281100
3.16-3.4813.20.06345300.931100
3.48-3.9912.80.05845630.9331100
3.99-5.0213.40.05446070.9021100
5.02-5012.10.04748160.661100

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS3

3is3


Resolution: 1.85→45.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.495 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18763 4568 5.2 %RANDOM
Rwork0.15096 ---
obs0.15285 84089 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.85→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7907 0 296 569 8772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177627
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.68511412
X-RAY DIFFRACTIONr_angle_other_deg1.4811.59917638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00551043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4422.072415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.889151301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1191552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021772
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_it1.8251.9194181
X-RAY DIFFRACTIONr_mcbond_other1.8251.9184180
X-RAY DIFFRACTIONr_mcangle_it2.6342.8655221
X-RAY DIFFRACTIONr_mcangle_other2.6332.8665222
X-RAY DIFFRACTIONr_scbond_it2.7092.2814211
X-RAY DIFFRACTIONr_scbond_other2.7082.2824212
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0533.3096192
X-RAY DIFFRACTIONr_long_range_B_refined5.38223.9879921
X-RAY DIFFRACTIONr_long_range_B_other5.38223.999922
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.894 Å
RfactorNum. reflection% reflection
Rfree0.242 334 -
Rwork0.195 5149 -
obs--82.82 %

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