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- PDB-3tjl: Crystal Structure of a Novel OYE from the Xylose-fermenting Fungu... -

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Basic information

Entry
Database: PDB / ID: 3tjl
TitleCrystal Structure of a Novel OYE from the Xylose-fermenting Fungus P. stipitis
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / Old yellow enzyme / Flavin mononucleotide / TIM barrel / NADPH oxidoreductase / Enone Reductase / Alkene reductase / stereocomplementarity / stereoselective / parallel alpha/beta barrel / biocatalysis / NADPH / FMN
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
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
FLAVIN MONONUCLEOTIDE / MALONIC ACID / NADPH dehydrogenase
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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.Z. / Stewart, J.D.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Derived calculations
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Sep 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_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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1569
Polymers45,2961
Non-polymers8608
Water9,278515
1
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,31218
Polymers90,5912
Non-polymers1,72116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/21
Buried area5180 Å2
ΔGint-116 kcal/mol
Surface area29530 Å2
Unit cell
Length a, b, c (Å)127.164, 127.164, 122.457
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-582-

HOH

21A-600-

HOH

31A-842-

HOH

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Components

#1: Protein NADPH dehydrogenase /


Mass: 45295.543 Da / Num. of mol.: 1 / Mutation: T169A
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-26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A3LT82, NADPH dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 3.16 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Sodium malonate 1-3% 2-propanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2011 / Details: Si 111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→44 Å / Num. obs: 92358 / % possible obs: 0.996 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: dev_845)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OYA

1oya


Resolution: 1.5→44 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 14.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1682 9236 10 %random
Rwork0.1428 ---
obs0.1454 92358 99.07 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.492 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.921 Å20 Å2-0 Å2
2--0.921 Å2-0 Å2
3----1.8419 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 56 515 3745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113373
X-RAY DIFFRACTIONf_angle_d1.3324606
X-RAY DIFFRACTIONf_dihedral_angle_d14.2831255
X-RAY DIFFRACTIONf_chiral_restr0.094509
X-RAY DIFFRACTIONf_plane_restr0.007601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.32522940.26932647X-RAY DIFFRACTION96
1.517-1.53490.28933030.23542726X-RAY DIFFRACTION98
1.5349-1.55360.25413030.21082725X-RAY DIFFRACTION100
1.5536-1.57320.25863060.20422756X-RAY DIFFRACTION100
1.5732-1.5940.23563060.18372761X-RAY DIFFRACTION100
1.594-1.61580.22653040.16672734X-RAY DIFFRACTION100
1.6158-1.63890.22323080.15552767X-RAY DIFFRACTION100
1.6389-1.66330.21663070.14822764X-RAY DIFFRACTION100
1.6633-1.68930.20453060.14152757X-RAY DIFFRACTION100
1.6893-1.7170.17233080.12672775X-RAY DIFFRACTION100
1.717-1.74660.17493090.12792767X-RAY DIFFRACTION100
1.7466-1.77840.17333060.12332758X-RAY DIFFRACTION100
1.7784-1.81260.16933070.11912763X-RAY DIFFRACTION100
1.8126-1.84960.19143070.12512762X-RAY DIFFRACTION100
1.8496-1.88980.15713060.12352765X-RAY DIFFRACTION100
1.8898-1.93380.15893090.12352777X-RAY DIFFRACTION100
1.9338-1.98210.17343090.12792780X-RAY DIFFRACTION100
1.9821-2.03570.1553070.12222767X-RAY DIFFRACTION100
2.0357-2.09560.173070.12882763X-RAY DIFFRACTION99
2.0956-2.16330.1513090.12912774X-RAY DIFFRACTION99
2.1633-2.24060.14683100.11762791X-RAY DIFFRACTION99
2.2406-2.33030.15443080.12362774X-RAY DIFFRACTION99
2.3303-2.43630.13933100.12622787X-RAY DIFFRACTION99
2.4363-2.56480.17343090.14112781X-RAY DIFFRACTION99
2.5648-2.72540.1873090.15422782X-RAY DIFFRACTION99
2.7254-2.93580.18253110.16222795X-RAY DIFFRACTION98
2.9358-3.23120.1863090.15482782X-RAY DIFFRACTION98
3.2312-3.69860.15263100.13952795X-RAY DIFFRACTION97
3.6986-4.6590.12343100.12392786X-RAY DIFFRACTION96
4.659-44.12270.17283290.16672961X-RAY DIFFRACTION96

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