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- PDB-4oaq: Crystal structure of the R-specific Carbonyl Reductase from Candi... -

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Basic information

Entry
Database: PDB / ID: 4oaq
TitleCrystal structure of the R-specific Carbonyl Reductase from Candida parapsilosis ATCC 7330
ComponentsR-specific carbonyl reductase
KeywordsOXIDOREDUCTASE / Rossman fold / Stereoselectivity / Zinc dependent carbonyl reductase / NADPH
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-NDP / Alcohol dehydrogenase GroES-like domain family protein
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.858 Å
AuthorsAggrawal, N. / Mandal, P.K. / Gautham, N. / Chadha, A.
Citation
Journal: To be Published
Title: Insights into the stereoselectivity of R-specific Carbonyl Reductase from Candida parapsilosis ATCC 7330: Biochemical Characterization and Crystal structure studies
Authors: Aggrawal, N. / Mandal, P.K. / Gautham, N. / Chadha, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330.
Authors: Aggarwal, N. / Mandal, P.K. / Gautham, N. / Chadha, A.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,76910
Polymers80,3182
Non-polymers1,4518
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-65 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.724, 99.896, 116.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein R-specific carbonyl reductase


Mass: 40159.188 Da / Num. of mol.: 2 / Fragment: Cinnamyl Carbonyl Reductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Strain: ATCC 7330 / Gene: CpCR / Plasmid: pGEX-6-P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: M4VRJ6, cinnamyl-alcohol dehydrogenase

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Non-polymers , 7 types, 572 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein sample (13.5 mg/ml) was mixed with an equal volume of reservoir solution and equilibrated against the latter. The reservoir solution consisted of 25%(w/v) PEG 4000 as a precipitant, ...Details: protein sample (13.5 mg/ml) was mixed with an equal volume of reservoir solution and equilibrated against the latter. The reservoir solution consisted of 25%(w/v) PEG 4000 as a precipitant, 0.1 M HEPES pH 7.5 as buffer, and 8% isopropanol and 0.1 mM ZnCl2 as additives., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 2012 / Details: Confocal Max-Flux (CMF)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.858→24.974 Å / Num. all: 65250 / Num. obs: 62705 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.46
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.13 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1piw

1piw


Resolution: 1.858→24.974 Å / SU ML: 0.25 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 3172 5.06 %Random
Rwork0.2014 ---
obs0.2038 62704 95.9 %-
all-65385 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.858→24.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5534 0 81 564 6179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085750
X-RAY DIFFRACTIONf_angle_d1.2257785
X-RAY DIFFRACTIONf_dihedral_angle_d15.1962077
X-RAY DIFFRACTIONf_chiral_restr0.084847
X-RAY DIFFRACTIONf_plane_restr0.0041015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.858-1.88570.34211410.292542X-RAY DIFFRACTION96
1.8857-1.91520.44661280.36712592X-RAY DIFFRACTION97
1.9152-1.94660.3721260.32252577X-RAY DIFFRACTION97
1.9466-1.98010.30961230.25882604X-RAY DIFFRACTION97
1.9801-2.01610.31381220.23312598X-RAY DIFFRACTION97
2.0161-2.05490.26771500.23722539X-RAY DIFFRACTION96
2.0549-2.09680.3071280.22072543X-RAY DIFFRACTION95
2.0968-2.14240.29411440.22312490X-RAY DIFFRACTION94
2.1424-2.19220.26771400.21722495X-RAY DIFFRACTION93
2.1922-2.24690.43571300.31422350X-RAY DIFFRACTION88
2.2469-2.30770.36661230.28822329X-RAY DIFFRACTION87
2.3077-2.37550.27471110.19292498X-RAY DIFFRACTION92
2.3755-2.45210.24081490.19692453X-RAY DIFFRACTION92
2.4521-2.53970.22031340.18262537X-RAY DIFFRACTION94
2.5397-2.64130.23461360.18882576X-RAY DIFFRACTION96
2.6413-2.76130.26851230.19382659X-RAY DIFFRACTION98
2.7613-2.90670.22671460.19052674X-RAY DIFFRACTION99
2.9067-3.08850.24541510.18332701X-RAY DIFFRACTION100
3.0885-3.32650.24461660.19522699X-RAY DIFFRACTION100
3.3265-3.66030.23611560.18832713X-RAY DIFFRACTION100
3.6603-4.18780.19611550.17272726X-RAY DIFFRACTION100
4.1878-5.2680.16271310.14512783X-RAY DIFFRACTION100
5.268-24.97620.20821590.17592854X-RAY DIFFRACTION98
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)
11.76190.31250.63642.23821.03372.1837-0.0270.030.0324-0.1134-0.10720.2988-0.027-0.120.1150.1138-0.0041-0.00340.0928-0.01710.144311.3953-24.0506-25.6237
26.06040.63380.23553.8238-0.78423.9509-0.1634-0.2361-0.10220.4535-0.16770.27240.3013-0.35130.30820.2129-0.05230.08950.224-0.07720.172910.728-13.24081.0855
33.28390.51845.21151.5211.469.924-0.1964-0.13080.42060.0792-0.18510.1598-0.354-0.20370.40530.0921-0.01490.03950.1585-0.04380.245718.1105-3.5859-4.8221
42.85590.10520.71790.44380.34992.0123-0.0265-0.13790.19610.1607-0.20360.5320.095-0.23190.20690.1614-0.00350.04910.1518-0.10440.34067.4497-18.2239-12.2997
52.00031.99982.00032.00011.99942.00054.10763.7003-5.57552.77552.3988-1.02946.82763.1584-6.55080.42370.1488-0.5060.4383-0.18730.723-4.554-28.6254-30.2762
61.394-0.4282-0.59722.9461-0.65463.0058-0.0953-0.16310.28570.13690.04710.1382-0.6433-0.28980.03760.24340.0541-0.04420.1429-0.05480.169546.334718.4074.5816
71.00570.46320.54471.67821.44183.4780.0202-0.1117-0.07720.11550.0161-0.02290.0664-0.0842-0.0330.0870.0190.00140.10310.03440.116245.92131.3461-2.3678
82.95951.48141.40661.7431.12592.9915-0.1190.02660.3094-0.1811-0.03790.1676-0.2317-0.13350.15210.11720.00050.01070.09680.01230.128835.4326-4.2379-13.7908
94.1603-0.3410.55835.02740.19154.7357-0.07230.12810.0888-0.1505-0.0046-0.258-0.31750.22780.06460.1595-0.04830.01550.10190.00390.126955.387414.712-8.3639
1021.99952.00042.00041.99992-2.4381-5.71012.92623.10980.2592-3.4718-3.9213-2.72062.17950.6280.1251-0.44680.4302-0.03630.510557.927122.48616.6159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 241 )
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 293 )
4X-RAY DIFFRACTION4chain 'A' and (resid 294 through 365 )
5X-RAY DIFFRACTION5chain 'A' and (resid 366 through 367 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 80 )
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 241 )
8X-RAY DIFFRACTION8chain 'B' and (resid 242 through 325 )
9X-RAY DIFFRACTION9chain 'B' and (resid 326 through 365 )
10X-RAY DIFFRACTION10chain 'B' and (resid 366 through 367 )

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