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- PDB-7c2o: Crystal structure of the R-specific Carbonyl Reductase from Candi... -

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Basic information

Entry
Database: PDB / ID: 7c2o
TitleCrystal structure of the R-specific Carbonyl Reductase from Candida parapsilosis ATCC 7330 without DTT
ComponentsR-specific carbonyl reductase
KeywordsOXIDOREDUCTASE / carbonyl reductase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / zinc ion binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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 ...: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
Chem-NDP / Alcohol dehydrogenase GroES-like domain family protein
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVinaykumar, K. / KanalElamparithi, B. / Chaudhury, D. / Gunasekaran, K. / Chadha, A.
CitationJournal: To Be Published
Title: Crystal structure of the R-specific Carbonyl Reductase from Candida parapsilosis ATCC 7330 without DTT
Authors: Vinaykumar, K. / KanalElamparithi, B. / Chaudhury, D. / Gunasekaran, K. / Chadha, A.
History
DepositionMay 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: R-specific carbonyl reductase
B: R-specific carbonyl reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7577
Polymers80,5772
Non-polymers1,1805
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-51 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.392, 100.950, 115.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein R-specific carbonyl reductase


Mass: 40288.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: CpCR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: M4VRJ6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22.5%(w/v) PEG 4000, 0.1M HEPES pH 7.5, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.9→33.13 Å / Num. obs: 17471 / % possible obs: 99.3 % / Redundancy: 3.86 % / Biso Wilson estimate: 47.62 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.17 / Net I/σ(I): 8.44
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.67 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 2331 / CC1/2: 0.69 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OAQ

4oaq


Resolution: 2.9→33.13 Å / SU ML: 0.4525 / Cross valid method: FREE R-VALUE / Phase error: 29.7708
RfactorNum. reflection% reflection
Rfree0.2958 1625 9.31 %
Rwork0.2385 --
obs0.2438 17462 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.78 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 18 131 5682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255683
X-RAY DIFFRACTIONf_angle_d0.49087698
X-RAY DIFFRACTIONf_chiral_restr0.0433833
X-RAY DIFFRACTIONf_plane_restr0.00261013
X-RAY DIFFRACTIONf_dihedral_angle_d10.9624799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.43821350.35061309X-RAY DIFFRACTION100
2.99-3.080.33231310.31621288X-RAY DIFFRACTION100
3.08-3.190.38541330.29591296X-RAY DIFFRACTION99.93
3.19-3.320.36691340.28131303X-RAY DIFFRACTION100
3.32-3.470.37761350.2821311X-RAY DIFFRACTION100
3.47-3.650.33831340.25841305X-RAY DIFFRACTION99.65
3.65-3.880.30431330.26051304X-RAY DIFFRACTION99.38
3.88-4.180.25011330.22911290X-RAY DIFFRACTION99.44
4.18-4.60.28781380.19011336X-RAY DIFFRACTION99.93
4.6-5.260.2561350.191324X-RAY DIFFRACTION99.86
5.26-6.620.23591390.21971356X-RAY DIFFRACTION100
6.62-33.130.23411450.19741415X-RAY DIFFRACTION98.98
Refinement TLS params.Method: refined / Origin x: 27.9238243078 Å / Origin y: -6.33291426732 Å / Origin z: -9.65537406691 Å
111213212223313233
T0.314641833048 Å20.0848117481806 Å20.0010817785571 Å2-0.290680637828 Å2-0.0650835879921 Å2--0.245291463158 Å2
L1.30456709393 °21.37202614242 °21.02432531137 °2-1.89103165081 °20.939827364478 °2--1.14451392848 °2
S0.0792437309851 Å °-0.404979633813 Å °0.053169299166 Å °0.00197404166287 Å °-0.261295166749 Å °0.0679006691122 Å °-0.0699952291746 Å °-0.369849968924 Å °0.121584244218 Å °
Refinement TLS groupSelection details: all

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