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- PDB-4rnw: Truncated version of the G303 Circular Permutation of Old Yellow ... -

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Basic information

Entry
Database: PDB / ID: 4rnw
TitleTruncated version of the G303 Circular Permutation of Old Yellow Enzyme
ComponentsNADPH dehydrogenase 1
KeywordsOXIDOREDUCTASE / CIRCULAR PERMUTATION / CATALYSIS / OLD YELLOW ENZYME / FLAVIN COFACTOR
Function / homologyNADPH dehydrogenase / NADPH dehydrogenase activity / Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / FLAVIN MONONUCLEOTIDE / NADPH dehydrogenase 1
Function and homology information
Biological speciesSaccharomyces pastorianus (lager yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,38426
Polymers86,7542
Non-polymers2,63124
Water16,772931
1
A: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,63012
Polymers43,3771
Non-polymers1,25311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADPH dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,75414
Polymers43,3771
Non-polymers1,37713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.247, 73.002, 84.742
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43376.820 Da / Num. of mol.: 2 / Fragment: UNP residues 307-397, 2-292
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.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→28.98 Å / Num. all: 110800 / Num. obs: 108578 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.9 / Num. unique all: 10639 / % possible all: 96.6

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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: 1.552→28.98 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1995 1.84 %RANDOM
Rwork0.1939 ---
obs0.1946 108291 97.65 %-
all-110700 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.552→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 172 931 7161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096392
X-RAY DIFFRACTIONf_angle_d1.2598638
X-RAY DIFFRACTIONf_dihedral_angle_d14.752344
X-RAY DIFFRACTIONf_chiral_restr0.09891
X-RAY DIFFRACTIONf_plane_restr0.0061115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.552-1.59080.3281370.25867352X-RAY DIFFRACTION95
1.5908-1.63380.2761410.23447433X-RAY DIFFRACTION96
1.6338-1.68190.25981400.21997483X-RAY DIFFRACTION97
1.6819-1.73620.28341420.20257511X-RAY DIFFRACTION96
1.7362-1.79820.24171410.19537473X-RAY DIFFRACTION97
1.7982-1.87020.25791380.19667511X-RAY DIFFRACTION96
1.8702-1.95530.24971420.19447518X-RAY DIFFRACTION98
1.9553-2.05830.22161430.18327600X-RAY DIFFRACTION98
2.0583-2.18730.21391440.17827684X-RAY DIFFRACTION99
2.1873-2.35610.22061440.18577676X-RAY DIFFRACTION99
2.3561-2.5930.24751460.19837719X-RAY DIFFRACTION99
2.593-2.96790.23841440.19567735X-RAY DIFFRACTION99
2.9679-3.7380.20481460.1857792X-RAY DIFFRACTION99
3.738-28.98550.21261470.19077809X-RAY DIFFRACTION99

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