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- PDB-4rnu: G303 Circular Permutation of Old Yellow Enzyme -

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Basic information

Entry
Database: PDB / ID: 4rnu
TitleG303 Circular Permutation of Old Yellow Enzyme
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / CIRCULAR PERMUTATION / CATALYSIS / OLD YELLOW ENZYME / FLAVIN COFACTOR
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 / PHOSPHATE ION / NADPH dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.677 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)181,97912
Polymers179,7744
Non-polymers2,2058
Water2,018112
1
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4953
Polymers44,9431
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4953
Polymers44,9431
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4953
Polymers44,9431
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4953
Polymers44,9431
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.662, 87.642, 113.572
Angle α, β, γ (deg.)69.32, 82.56, 90.02
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
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: Mar 25, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.677→38.78 Å / Num. all: 45790 / Num. obs: 42123 / % possible obs: 92 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 13.8
Reflection shellResolution: 2.677→2.79 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4241 / % possible all: 92.5

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OYA

1oya


Resolution: 2.677→38.78 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 37.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1823 5.13 %RANDOM
Rwork0.2472 ---
obs0.2483 36855 91.28 %-
all-45790 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.677→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11891 0 144 112 12147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212338
X-RAY DIFFRACTIONf_angle_d0.50216784
X-RAY DIFFRACTIONf_dihedral_angle_d11.9844408
X-RAY DIFFRACTIONf_chiral_restr0.0361763
X-RAY DIFFRACTIONf_plane_restr0.0022197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.677-2.74440.38641500.34142728X-RAY DIFFRACTION84
2.7444-2.81850.36771300.32082902X-RAY DIFFRACTION88
2.8185-2.90140.37011440.32912845X-RAY DIFFRACTION87
2.9014-2.99490.33481340.30862850X-RAY DIFFRACTION87
2.9949-3.10180.38681440.29382811X-RAY DIFFRACTION86
3.1018-3.22590.29781280.2952842X-RAY DIFFRACTION86
3.2259-3.37240.29371470.28732808X-RAY DIFFRACTION86
3.3724-3.54990.31571230.27492814X-RAY DIFFRACTION85
3.5499-3.77180.4662960.40741978X-RAY DIFFRACTION60
3.7718-4.06220.28941510.22332940X-RAY DIFFRACTION90
4.0622-4.46940.24781570.19373086X-RAY DIFFRACTION94
4.4694-5.11260.20131570.18883106X-RAY DIFFRACTION95
5.1126-6.4280.25471500.22253117X-RAY DIFFRACTION95
6.428-27.65050.22021600.1863119X-RAY DIFFRACTION95
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)
12.334-0.0609-0.2671.90661.09642.94320.26980.1874-0.1411-1.13680.1188-0.36580.51730.178-0.37881.05740.04260.01910.3676-0.04720.39338.09-19.56462.7424
22.9095-0.97640.02366.14610.19252.66640.1458-0.4751-0.08540.45560.14430.16630.1812-0.0461-0.28650.483-0.0097-0.00590.3332-0.00750.316532.3438-11.562983.0147
31.90090.7652-0.48524.68060.08153.0320.3241-0.1650.37941.00960.1495-0.1256-0.61190.2701-0.39070.74680.1145-0.00240.2861-0.06360.675658.09398.4194121.423
41.87880.76970.42144.663-0.32021.44910.18320.2675-0.0552-0.2570.0743-0.3307-0.11850.0868-0.22490.47640.2342-0.01460.3187-0.01590.381958.1281-3.6869107.4134
52.50150.62880.1583.1139-1.82122.3028-0.10350.37710.6005-1.36310.20950.6118-0.4801-0.2654-0.05471.0502-0.01250.02260.33030.02611.143365.959130.985862.8804
61.4137-0.0510.26215.3112-0.17292.0572-0.0635-0.37330.64730.62020.2816-0.1572-0.3945-0.0423-0.13510.73730.04430.18480.3166-0.18180.767470.684923.011982.9692
72.4861-0.0280.28082.6879-1.73811.1419-0.0396-0.8459-0.75171.98650.0750.6250.6968-0.3106-0.24891.79330.09680.1240.50320.2170.800544.488746.8411129.2533
81.683-0.00370.24435.58070.01391.8477-0.06220.2314-0.9834-0.26710.2196-0.02780.5012-0.1121-0.07590.69090.1232-0.08460.2627-0.10410.893845.231850.3052107.8775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:214)
2X-RAY DIFFRACTION2(chain A and resid 215:390)
3X-RAY DIFFRACTION3(chain B and resid 6:257)
4X-RAY DIFFRACTION4(chain B and resid 258:390)
5X-RAY DIFFRACTION5(chain C and resid 6:215)
6X-RAY DIFFRACTION6(chain C and resid 216:390)
7X-RAY DIFFRACTION7(chain D and resid 6:165)
8X-RAY DIFFRACTION8(chain D and resid 166:390)

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