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- PDB-3wg6: Crystal structure of conjugated polyketone reductase C1 from Cand... -

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Basic information

Entry
Database: PDB / ID: 3wg6
TitleCrystal structure of conjugated polyketone reductase C1 from Candida parapsilosis complexed with NADPH
ComponentsConjugated polyketone reductase C1
KeywordsOXIDOREDUCTASE / AKR SUPERFAMILY / TIM BARREL / D-PANTOYL LACTONE
Function / homology
Function and homology information


2-dehydropantolactone reductase / 2-dehydropantolactone reductase (A-specific) activity / oxidoreductase activity, acting on NAD(P)H as acceptor / ketone metabolic process / : / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
Aldo-keto reductase family 3C2/3 / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / NADPH-dependent conjugated polyketone reductase C1
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQin, H.-M. / Yamamura, A. / Miyakawa, T. / Maruoka, S. / Ohtsuka, J. / Nagata, K. / Kataoka, M. / Shimizu, S. / Tanokura, M.
CitationJournal: Proteins / Year: 2013
Title: Crystal structure of conjugated polyketone reductase (CPR-C1) from Candida parapsilosis IFO 0708 complexed with NADPH.
Authors: Qin, H.M. / Yamamura, A. / Miyakawa, T. / Kataoka, M. / Maruoka, S. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M.
History
DepositionJul 28, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conjugated polyketone reductase C1
B: Conjugated polyketone reductase C1
C: Conjugated polyketone reductase C1
D: Conjugated polyketone reductase C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,2668
Polymers139,2854
Non-polymers2,9824
Water5,873326
1
A: Conjugated polyketone reductase C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5672
Polymers34,8211
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conjugated polyketone reductase C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5672
Polymers34,8211
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Conjugated polyketone reductase C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5672
Polymers34,8211
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Conjugated polyketone reductase C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5672
Polymers34,8211
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.070, 84.930, 136.160
Angle α, β, γ (deg.)90.00, 96.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Conjugated polyketone reductase C1


Mass: 34821.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Strain: IFO 0708 / Gene: cpr-c1 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q76L37
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: 5MM NADPH, 0.1M TRIS-HCL, 25% PEG 3350, 5MM NACL, PH 8.5, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 67499 / % possible obs: 99.1 %

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.719 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3424 5.1 %RANDOM
Rwork0.182 ---
obs0.185 67495 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9586 0 192 326 10104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0229980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.99313497
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31551185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5624.969491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.299151799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2711552
X-RAY DIFFRACTIONr_chiral_restr0.1270.21459
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217486
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9151.55886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59929484
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.84934094
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3444.54013
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 249 -
Rwork0.207 4618 -
obs--98.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9758-0.55790.42781.0209-0.3431.53450.06420.02020.0563-0.1172-0.01410.00520.1593-0.064-0.05010.0567-0.05440.00940.14970.06340.11491.658543.5951-63.4999
21.35340.0054-0.16870.85890.20211.5057-0.09410.0016-0.03220.17670.04920.00290.08560.00820.04490.20220.06040.00750.0211-0.01040.06155.781840.16521.8005
30.65760.0489-0.09530.91580.24611.5285-0.00960.04780.0090.13850.067-0.07830.21840.1942-0.05740.0650.0078-0.01870.0584-0.01340.06320.416521.4403-35.3856
41.3860.14520.13810.93660.33331.5689-0.06080.03230.24630.09650.0374-0.1048-0.29180.130.02340.1217-0.0564-0.03070.0417-0.00120.165825.662557.5426-29.0057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 304
2X-RAY DIFFRACTION2B6 - 304
3X-RAY DIFFRACTION3C6 - 303
4X-RAY DIFFRACTION4D6 - 303

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