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- PDB-8hfj: Crystal Structure of CbAR mutant (H162F) in complex with NADP+ an... -

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Basic information

Entry
Database: PDB / ID: 8hfj
TitleCrystal Structure of CbAR mutant (H162F) in complex with NADP+ and a bulky 1,3-cyclodiketone
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
Chem-L7Z / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Versicolorin reductase
Similarity search - Component
Biological speciesCercospora sp. JNU001 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsHou, X.D. / Yin, D.J. / 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
DepositionNov 10, 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
A: Versicolorin reductase
B: Versicolorin reductase
C: Versicolorin reductase
D: Versicolorin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,90610
Polymers120,5004
Non-polymers3,4066
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18700 Å2
ΔGint-100 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.920, 124.920, 133.778
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: 30124.939 Da / Num. of mol.: 4 / Mutation: H162F
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: Chemical ChemComp-L7Z / 2-methyl-2-[(4-methylphenyl)methyl]cyclopentane-1,3-dione


Mass: 216.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 43.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M HEPES pH 7.5, 15% isopropanol and 19% 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, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.75→24.11 Å / Num. obs: 26700 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.983 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
2.75-2.846533150.231
2.846-2.96479810.2231
2.96-3.094426830.2161
3.094-3.257373700.2091
3.257-3.461320400.2011
3.461-3.727267470.1921
3.727-4.1214170.1831
4.1-4.69161050.1731
4.69-5.894107560.1681

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Processing

Software
NameVersionClassification
SAINTdata scaling
REFMAC5.5refinement
SAINTdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YB1

7yb1


Resolution: 2.75→24.11 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.85 / SU B: 18.088 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27012 1383 4.9 %RANDOM
Rwork0.2048 ---
obs0.20806 26700 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.907 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0 Å2-0 Å2
2--0.67 Å2-0 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 2.75→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 224 103 7986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138059
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177362
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.67510950
X-RAY DIFFRACTIONr_angle_other_deg1.2681.60117008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.33851018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08122.174391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.222151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7651548
X-RAY DIFFRACTIONr_chiral_restr0.0680.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021707
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_it1.2992.1194090
X-RAY DIFFRACTIONr_mcbond_other1.2992.1184089
X-RAY DIFFRACTIONr_mcangle_it2.1623.1675102
X-RAY DIFFRACTIONr_mcangle_other2.1623.1685103
X-RAY DIFFRACTIONr_scbond_it1.3672.2513969
X-RAY DIFFRACTIONr_scbond_other1.3692.2533970
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2893.3425849
X-RAY DIFFRACTIONr_long_range_B_refined4.20225.2468707
X-RAY DIFFRACTIONr_long_range_B_other4.20225.2538708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 103 -
Rwork0.274 1950 -
obs--99.85 %

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