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- PDB-7yb1: Crystal Structure of anthrol reductase (CbAR) in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 7yb1
TitleCrystal Structure of anthrol reductase (CbAR) in complex with NADP+
ComponentsVersicolorin reductase
KeywordsOXIDOREDUCTASE / anthrol reductase / chiral alcohol / emodin
Function / homologyoxidoreductase activity, acting on CH-OH group of donors / 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 / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Versicolorin reductase
Function and homology information
Biological speciesCercospora sp. JNU001 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,4378
Polymers120,4644
Non-polymers2,9744
Water30617
1
A: Versicolorin reductase
B: Versicolorin reductase
C: Versicolorin reductase
hetero molecules

D: Versicolorin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4378
Polymers120,4644
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1/2,y+1/2,-z+1/41
Buried area13880 Å2
ΔGint-77 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.624, 124.624, 134.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
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: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.542 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.988→23.66 Å / Num. obs: 15527 / % possible obs: 99.17 % / Redundancy: 5.13 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
2.988-3.095413620.6491
3.095-3.218374620.61
3.218-3.364333260.5741
3.364-3.541291680.471
3.541-3.762250370.4071
3.762-4.051208930.3791
4.051-4.457167520.3211
4.457-5.096125890.311
5.096-6.39984130.3621

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTV8.38Adata scaling
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS3

3is3


Resolution: 3.3→23.66 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.791 / SU B: 37.879 / SU ML: 0.606 / Cross valid method: THROUGHOUT / ESU R Free: 0.678 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 887 5.4 %RANDOM
Rwork0.20599 ---
obs0.21025 15527 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 3.3→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7525 0 192 17 7734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177293
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.6710712
X-RAY DIFFRACTIONr_angle_other_deg1.1861.59716857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3345995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06921.934393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.048151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8621552
X-RAY DIFFRACTIONr_chiral_restr0.0610.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021677
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_it0.8581.6784000
X-RAY DIFFRACTIONr_mcbond_other0.8581.6783999
X-RAY DIFFRACTIONr_mcangle_it1.4992.514983
X-RAY DIFFRACTIONr_mcangle_other1.4992.5114984
X-RAY DIFFRACTIONr_scbond_it0.8241.7623900
X-RAY DIFFRACTIONr_scbond_other0.8241.7623898
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4592.6135730
X-RAY DIFFRACTIONr_long_range_B_refined3.06319.688526
X-RAY DIFFRACTIONr_long_range_B_other3.06319.6798527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 60 -
Rwork0.273 1132 -
obs--100 %

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