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- PDB-4c4o: Structure of carbonyl reductase CPCR2 from Candida parapsilosis i... -

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Basic information

Entry
Database: PDB / ID: 4c4o
TitleStructure of carbonyl reductase CPCR2 from Candida parapsilosis in complex with NADH
ComponentsCARBONYL REDUCTASE CPCR2
KeywordsOXIDOREDUCTASE / ALCOHOL DEHYDROGENASE / MEDIUM CHAIN REDUCTASE / KETOREDUCTASE / NADH
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase GroES-like domain family protein
Similarity search - Component
Biological speciesCANDIDA PARAPSILOSIS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMan, H. / Loderer, C. / Ansorge-Schumacher, M. / Grogan, G.
CitationJournal: Chemcatchem / Year: 2014
Title: Structure of Nadh-Dependent Carbonyl Reductase (Cpcr2) from Candida Parapsilosis Provides Insight Into Mutations that Improve Catalytic Properties
Authors: Man, H. / Loderer, C. / Ansorge-Schumacher, M.B. / Grogan, G.
History
DepositionSep 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Data collection
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: CARBONYL REDUCTASE CPCR2
B: CARBONYL REDUCTASE CPCR2
C: CARBONYL REDUCTASE CPCR2
D: CARBONYL REDUCTASE CPCR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,63123
Polymers144,0174
Non-polymers3,61519
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16180 Å2
ΔGint-234.5 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.720, 88.840, 118.200
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9114, -0.1537, 0.3818), (-0.1352, -0.988, -0.07501), (0.3887, 0.01676, -0.9212)-11.41, 1.82, 58.52
2given(-0.9209, 0.1975, -0.3362), (0.2755, -0.2804, -0.9195), (-0.2759, -0.9393, 0.2038)-28.26, 31.59, 15.82
3given(-0.9907, -0.0913, -0.1007), (-0.1212, 0.2591, 0.9582), (0.0614, 0.9615, -0.2678)-36.08, -27.22, 31.39

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Components

#1: Protein
CARBONYL REDUCTASE CPCR2


Mass: 36004.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA PARAPSILOSIS (yeast) / Strain: IFO 1396 / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O42703, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M TRIS/HCL PH 8.0, 30% (W/V) PEG 3350 AND 2-METHYL-1,4-PENTANEDIOL (40% V/V); PROTEIN AT 70 MG/ML; SOAKED IN 10 MM NADH FOR 5 MIN PRIOR TO FLASH COOLING

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.05→58.13 Å / Num. obs: 85098 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7
Reflection shellResolution: 2.05→2.13 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RJW

1rjw


Resolution: 2.05→58.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.903 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24073 4253 5 %RANDOM
Rwork0.20482 ---
obs0.20663 80823 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.865 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20.59 Å2
2--0.01 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.05→58.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8780 0 201 247 9228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0199261
X-RAY DIFFRACTIONr_bond_other_d0.0080.028439
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.98812596
X-RAY DIFFRACTIONr_angle_other_deg1.453.00219284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29551230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19824.927341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg301533
X-RAY DIFFRACTIONr_chiral_restr0.130.21450
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02110692
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022000
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_it4.144.5454968
X-RAY DIFFRACTIONr_mcbond_other4.1374.5444967
X-RAY DIFFRACTIONr_mcangle_it5.56.7826179
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5234.6554293
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 289 -
Rwork0.298 5968 -
obs--99.95 %

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