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- PDB-3wlf: Crystal structure of (R)-carbonyl reductase from Candida Parapsil... -

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Basic information

Entry
Database: PDB / ID: 3wlf
TitleCrystal structure of (R)-carbonyl reductase from Candida Parapsilosis in complex with (R)-1-phenyl-1,2-ethanediol
Components(R)-specific carbonyl reductase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / carbonyl reductase
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / nucleotide binding / zinc ion binding / cytoplasm
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(1R)-1-phenylethane-1,2-diol / (R)-specific carbonyl reductase
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, S.S. / Nie, Y. / Xu, Y. / Zhang, R.Z. / Huang, C.H. / Chan, H.C. / Guo, R.T. / Xiao, R.
CitationJournal: Chem.Commun.(Camb.) / Year: 2014
Title: Unconserved substrate-binding sites direct the stereoselectivity of medium-chain alcohol dehydrogenase
Authors: Wang, S.S. / Nie, Y. / Xu, Y. / Zhang, R.Z. / Ko, T.P. / Huang, C.H. / Chan, H.C. / Guo, R.T. / Xiao, R.
History
DepositionNov 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (R)-specific carbonyl reductase
B: (R)-specific carbonyl reductase
C: (R)-specific carbonyl reductase
D: (R)-specific carbonyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,46216
Polymers145,3864
Non-polymers1,07612
Water19,1501063
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-36 kcal/mol
Surface area48900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.493, 103.722, 141.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
(R)-specific carbonyl reductase / 1-phenyl-1 / 2-ethanediol dehydrogenase


Mass: 36346.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Strain: CCTCC M203011 / Gene: CPRADH / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1X808, alcohol dehydrogenase
#2: Chemical
ChemComp-FEH / (1R)-1-phenylethane-1,2-diol


Mass: 138.164 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1063 / 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: 48.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M sodium malonate, 12%(w/v) PEG3350, 2%(w/v) PEG10000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 62316 / Num. obs: 61940 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 30.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.6 / Num. unique all: 6126 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WLE

3wle


Resolution: 2.3→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 3028 4.9 %RANDOM
Rwork0.2059 ---
all-61940 --
obs-60076 97 %-
Solvent computationBsol: 39.9966 Å2
Displacement parametersBiso max: 92.5 Å2 / Biso mean: 30.7292 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.631 Å20 Å20 Å2
2--2.819 Å20 Å2
3----7.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10049 0 48 1063 11160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3741.5
X-RAY DIFFRACTIONc_scbond_it1.9692
X-RAY DIFFRACTIONc_mcangle_it2.2722
X-RAY DIFFRACTIONc_scangle_it2.8012.5
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection
Rfree0.314 294
Rwork0.244 -
obs-5701

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