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- PDB-4df2: P. stipitis OYE2.6 complexed with p-Chlorophenol -

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Basic information

Entry
Database: PDB / ID: 4df2
TitleP. stipitis OYE2.6 complexed with p-Chlorophenol
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / TIM barrel / FMN / NAD(P)H / cytosol
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-chlorophenol / FLAVIN MONONUCLEOTIDE / MALONIC ACID / NADPH dehydrogenase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.021 Å
AuthorsPompeu, Y.A. / Stewart, J.D.
CitationJournal: Adv.Synth.Catal. / Year: 2012
Title: Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions
Authors: Pompeu, Y.A. / Sullivan, B. / Walton, A. / Stewart, J.D.
History
DepositionJan 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Non-polymer description
Revision 1.2Sep 13, 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_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_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.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_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_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: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1657
Polymers45,3261
Non-polymers8396
Water7,134396
1
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,32914
Polymers90,6512
Non-polymers1,67812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_557x-y,-y,-z+21
Buried area4150 Å2
ΔGint-76 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.736, 127.736, 123.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-655-

HOH

21A-723-

HOH

31A-891-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NADPH dehydrogenase


Mass: 45325.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: OYE2.6, PICST_44614 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A3LT82

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Non-polymers , 5 types, 402 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-4CH / 4-chlorophenol


Mass: 128.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5ClO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3M malonate, 1% iPrOH pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2011 / Details: monochromatic CuKa
RadiationMonochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.95→44 Å / Num. all: 39462 / Num. obs: 38159 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rsym value: 0.093
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3825 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TJL

3tjl


Resolution: 2.021→24.86 Å / SU ML: 0.22 / Cross valid method: throughout refinement / σ(F): 1.34 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3815 10 %random 10%
Rwork0.1604 ---
obs0.1642 38149 96.7 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.746 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0112 Å2-0 Å20 Å2
2--1.0112 Å20 Å2
3----2.0224 Å2
Refinement stepCycle: LAST / Resolution: 2.021→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 55 396 3625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073357
X-RAY DIFFRACTIONf_angle_d1.0494578
X-RAY DIFFRACTIONf_dihedral_angle_d13.5731231
X-RAY DIFFRACTIONf_chiral_restr0.079504
X-RAY DIFFRACTIONf_plane_restr0.004593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0209-2.04650.26871400.24231269X-RAY DIFFRACTION99
2.0465-2.07340.27851430.23451276X-RAY DIFFRACTION99
2.0734-2.10180.29811390.22291258X-RAY DIFFRACTION99
2.1018-2.13180.25091420.19611279X-RAY DIFFRACTION99
2.1318-2.16360.23751410.18341268X-RAY DIFFRACTION99
2.1636-2.19740.22591430.17721283X-RAY DIFFRACTION99
2.1974-2.23340.21371410.1671262X-RAY DIFFRACTION99
2.2334-2.27190.21811430.16091294X-RAY DIFFRACTION99
2.2719-2.31320.21511420.16771281X-RAY DIFFRACTION99
2.3132-2.35760.20531410.15631262X-RAY DIFFRACTION99
2.3576-2.40570.21381440.15881297X-RAY DIFFRACTION98
2.4057-2.4580.22481410.15741269X-RAY DIFFRACTION98
2.458-2.51510.21461420.16621277X-RAY DIFFRACTION98
2.5151-2.5780.20751420.16331273X-RAY DIFFRACTION98
2.578-2.64760.20431410.16321275X-RAY DIFFRACTION98
2.6476-2.72540.24121440.16481290X-RAY DIFFRACTION98
2.7254-2.81330.21261400.1781266X-RAY DIFFRACTION97
2.8133-2.91370.20171420.16591279X-RAY DIFFRACTION97
2.9137-3.03010.20461410.17711257X-RAY DIFFRACTION97
3.0301-3.16780.22551420.17441283X-RAY DIFFRACTION96
3.1678-3.33440.21471400.16921258X-RAY DIFFRACTION96
3.3344-3.54280.18651400.16211270X-RAY DIFFRACTION95
3.5428-3.81540.16541400.14691256X-RAY DIFFRACTION95
3.8154-4.19770.16371370.12681238X-RAY DIFFRACTION93
4.1977-4.80130.15091410.11921269X-RAY DIFFRACTION92
4.8013-6.03490.15471400.14251265X-RAY DIFFRACTION92
6.0349-24.86220.19681430.17281280X-RAY DIFFRACTION87

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