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- PDB-4rnv: G303 Circular Permutation of Old Yellow Enzyme with the Inhibitor... -

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Basic information

Entry
Database: PDB / ID: 4rnv
TitleG303 Circular Permutation of Old Yellow Enzyme with the Inhibitor p-Hydroxybenzaldehyde
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE/Inhibitor / CIRCULAR PERMUTATION / CATALYSIS / OLD YELLOW ENZYME / FLAVIN COFACTOR / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


NADPH dehydrogenase / 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-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / P-HYDROXYBENZALDEHYDE / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.473 Å
AuthorsHorton, J.R. / Daugherty, A.B. / Cheng, X. / Lutz, S.
CitationJournal: ACS Catal / Year: 2015
Title: STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME.
Authors: Daugherty, A.B. / Horton, J.R. / Cheng, X. / Lutz, S.
History
DepositionOct 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / 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 / _entity.formula_weight / _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 1
B: NADPH dehydrogenase 1
C: NADPH dehydrogenase 1
D: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,08812
Polymers179,7744
Non-polymers2,3148
Water4,828268
1
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5223
Polymers44,9431
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5223
Polymers44,9431
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5223
Polymers44,9431
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5223
Polymers44,9431
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.591, 88.076, 105.617
Angle α, β, γ (deg.)89.45, 81.43, 89.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NADPH dehydrogenase 1 / Old yellow enzyme 1


Mass: 44943.430 Da / Num. of mol.: 4 / Fragment: UNP residues 303-397, 2-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces pastorianus (lager yeast)
Gene: OYE1 / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q02899, NADPH dehydrogenase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→34.811 Å / Num. all: 57560 / Num. obs: 56814 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.8
Reflection shellResolution: 2.47→2.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5641 / % possible all: 97.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OYA

1oya


Resolution: 2.473→34.811 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 1982 3.49 %RANDOM
Rwork0.2156 ---
obs0.2168 56763 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.473→34.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 160 268 12572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212616
X-RAY DIFFRACTIONf_angle_d0.53817108
X-RAY DIFFRACTIONf_dihedral_angle_d12.5484600
X-RAY DIFFRACTIONf_chiral_restr0.0231776
X-RAY DIFFRACTIONf_plane_restr0.0022228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.473-2.53450.38781040.30373544X-RAY DIFFRACTION86
2.5345-2.60310.35191640.30063800X-RAY DIFFRACTION98
2.6031-2.67960.29071370.2844025X-RAY DIFFRACTION98
2.6796-2.76610.31061290.27183843X-RAY DIFFRACTION98
2.7661-2.86490.31251470.26353978X-RAY DIFFRACTION98
2.8649-2.97950.27971330.25923920X-RAY DIFFRACTION98
2.9795-3.11510.25351420.2373930X-RAY DIFFRACTION98
3.1151-3.27920.28681820.24583914X-RAY DIFFRACTION99
3.2792-3.48450.29341130.22954006X-RAY DIFFRACTION99
3.4845-3.75320.2811120.21073952X-RAY DIFFRACTION99
3.7532-4.13040.1762070.1843941X-RAY DIFFRACTION99
4.1304-4.72680.23021530.18053930X-RAY DIFFRACTION99
4.7268-5.95040.1758560.17864061X-RAY DIFFRACTION99
5.9504-34.81420.22312030.1783937X-RAY DIFFRACTION100
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)
11.07540.58950.08030.8162-0.50921.186-0.0369-0.09770.07731.02960.0376-0.00850.1685-0.1097-0.01970.7482-0.00250.07530.3810.01210.1778-33.1834-18.5446-58.5066
21.0233-0.1008-0.07431.9041-0.05971.43240.0598-0.1966-0.08560.948-0.05770.46680.2283-0.0754-0.0950.7047-0.05410.13380.37810.01690.2658-38.609-25.6687-58.788
31.51490.6378-0.55312.7911-0.31851.0752-0.12560.0471-0.4288-0.08590.17870.47080.4842-0.0805-0.1220.359-0.06890.02010.356-0.06790.2453-39.089-27.5848-76.2329
42.23920.9084-0.24172.1608-0.72961.1927-0.03650.8159-0.8131-1.36850.0617-0.28030.499-0.03350.05540.5755-0.1115-0.00540.4802-0.10740.2498-30.2836-21.8351-88.749
51.3307-0.3201-0.08732.5157-0.19671.1808-0.08820.03880.0133-0.27310.09250.22060.0174-0.0229-0.00570.2260.0153-0.04760.28550.01690.2486-33.0536-11.4152-80.8134
61.79240.8972-0.87171.65940.51591.4859-0.01520.23510.2040.24440.1320.3692-0.0731-0.0558-0.08090.1814-0.03140.04290.29450.01590.2751-36.8892-4.8352-74.2401
72.0123-0.55950.10492.2852-0.50071.64160.28330.38970.1008-1.1602-0.16460.2587-0.2878-0.05090.04210.73620.0765-0.14130.5066-0.00540.2474-12.7471-38.2561-128.5617
82.5468-1.35510.5714.7812-0.2391.3016-0.173-0.1882-0.02960.45470.20920.5659-0.3009-0.1027-0.02910.2624-0.00520.04960.322-0.010.2138-12.408-41.974-107.2866
90.5441-0.1502-0.51821.13710.39220.79190.0605-0.29870.31940.92670.0991-0.2158-0.09860.1926-0.17440.6978-0.0413-0.0560.3949-0.08250.4697-23.6014-71.8951-57.9605
100.85370.20680.14181.0872-0.19411.09720.40580.00420.55311.190.0137-0.11020.34960.1184-0.29371.32710.08940.13360.5425-0.15491.1431-27.9015-52.164-53.012
111.5134-0.5595-0.89542.18720.27851.4280.2299-0.38371.37970.75020.1992-0.6039-0.36290.0728-0.26440.5157-0.10050.00780.3611-0.04871.0867-17.8024-58.7385-65.4826
121.52510.0102-1.22062.202-0.37371.46980.48510.00521.41830.3184-0.0353-0.2637-0.54680.38990.69460.4025-0.00720.08260.23320.12071.3099-16.8766-55.4979-74.1392
131.6470.6832-0.40881.20211.13522.79390.14811.10521.4447-0.758-0.1020.0592-1.1596-0.4223-0.22030.1983-0.00520.28690.34910.54181.2213-27.3589-60.8924-88.5303
140.99290.27720.20131.9338-0.49851.12470.11970.03240.66790.06420.0153-0.27960.02280.0543-0.11290.20760.01790.08440.31340.05470.5935-23.4702-74.0838-78.5389
150.8510.46930.45122.0151-0.40380.66510.08070.358-0.6971-1.59050.0048-0.24940.51030.125-0.00541.11540.09610.08220.5754-0.15320.8293-44.8113-86.1143-128.0017
161.8944-0.22910.25172.7412-0.73121.53290.1433-0.2127-0.9095-0.1806-0.00190.020.2831-0.0083-0.05370.2789-0.0337-0.06940.3450.09740.8659-45.9041-82.1311-106.926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 281 )
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 359 )
6X-RAY DIFFRACTION6chain 'A' and (resid 360 through 390 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 159 )
8X-RAY DIFFRACTION8chain 'B' and (resid 160 through 390 )
9X-RAY DIFFRACTION9chain 'C' and (resid 6 through 62 )
10X-RAY DIFFRACTION10chain 'C' and (resid 63 through 105 )
11X-RAY DIFFRACTION11chain 'C' and (resid 106 through 189 )
12X-RAY DIFFRACTION12chain 'C' and (resid 190 through 228 )
13X-RAY DIFFRACTION13chain 'C' and (resid 229 through 281 )
14X-RAY DIFFRACTION14chain 'C' and (resid 282 through 390 )
15X-RAY DIFFRACTION15chain 'D' and (resid 6 through 178 )
16X-RAY DIFFRACTION16chain 'D' and (resid 179 through 390 )

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