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- PDB-3gr8: Structure of OYE from Geobacillus kaustophilus, orthorhombic crys... -

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Basic information

Entry
Database: PDB / ID: 3gr8
TitleStructure of OYE from Geobacillus kaustophilus, orthorhombic crystal form
ComponentsNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / FLAVIN / FMN / BETA-ALPHA-BARREL / Flavoprotein / NADP
Function / homology
Function and homology information


NADPH dehydrogenase / NADPH dehydrogenase activity / response to toxic substance / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase, bacteria / NADPH dehydrogenase YqjM-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 / NADPH dehydrogenase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsUhl, M.K. / Gruber, K.
CitationJournal: ADV.SYNTH.CATAL. / Year: 2011
Title: Old Yellow Enzyme-Catalyzed Dehydrogenation of Saturated Ketones
Authors: Schittmayer, M. / Zach, S. / Winkler, M. / Winkler, A. / Macheroux, P. / Uhl, M.K. / Gruber, K. / Kambourakis, S. / Rozzell, D. / Glieder, A.
History
DepositionMar 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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
B: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8797
Polymers75,4522
Non-polymers1,4275
Water4,756264
1
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules

B: NADPH dehydrogenase
hetero molecules

B: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,75814
Polymers150,9034
Non-polymers2,85410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
crystal symmetry operation8_554x,-y,-z-1/21
Buried area12300 Å2
ΔGint-42 kcal/mol
Surface area45840 Å2
MethodPISA
2
A: NADPH dehydrogenase
hetero molecules

A: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,39310
Polymers75,4522
Non-polymers1,9428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area4880 Å2
ΔGint-9 kcal/mol
Surface area24100 Å2
MethodPISA
3
B: NADPH dehydrogenase
hetero molecules

B: NADPH dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3644
Polymers75,4522
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1/2,z1
Buried area4490 Å2
ΔGint-21 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.394, 151.930, 143.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein NADPH dehydrogenase / GkOYE / Xenobiotic reductase


Mass: 37725.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: namA / Plasmid: pEamTA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q5KXG9, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 50mM Bis-Tris, 50mM ammonium sulfate, 30% v/v pentaerythritole ethoxylate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.5→37 Å / Num. all: 30975 / Num. obs: 30975 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 21.815 Å2 / Rsym value: 0.166 / Net I/σ(I): 4.4
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.53 / % possible all: 83.7

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1z41

1z41


Resolution: 2.5→36.214 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.878 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1562 5.04 %random
Rwork0.188 ---
all-30975 --
obs-30975 97.61 %-
Solvent computationBsol: 40.01 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 108.09 Å2 / Biso mean: 22.127 Å2 / Biso min: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.046 Å20 Å20 Å2
2--0.059 Å20 Å2
3---0.986 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 95 264 5675
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d11
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0431
X-RAY DIFFRACTIONf_dihedral_angle_d17.0511
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.1161
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.496-2.510.236376X-RAY DIFFRACTION5973
2.51-2.5250.23386X-RAY DIFFRACTION5975
2.525-2.540.224408X-RAY DIFFRACTION5976
2.54-2.5550.223401X-RAY DIFFRACTION5975
2.555-2.5710.216411X-RAY DIFFRACTION5977
2.571-2.5870.222382X-RAY DIFFRACTION5974
2.587-2.6030.223423X-RAY DIFFRACTION5978
2.603-2.620.209516X-RAY DIFFRACTION5995
2.62-2.6380.221490X-RAY DIFFRACTION5994
2.638-2.6550.216509X-RAY DIFFRACTION5995
2.655-2.6740.193504X-RAY DIFFRACTION5995
2.674-2.6930.197489X-RAY DIFFRACTION5994
2.693-2.7120.207492X-RAY DIFFRACTION5995
2.712-2.7320.21527X-RAY DIFFRACTION5996
2.732-2.7520.227502X-RAY DIFFRACTION5994
2.752-2.7730.217493X-RAY DIFFRACTION5995
2.773-2.7950.222510X-RAY DIFFRACTION5995
2.795-2.8180.216519X-RAY DIFFRACTION5997
2.818-2.8410.199504X-RAY DIFFRACTION5997
2.841-2.8650.216504X-RAY DIFFRACTION5995
2.865-2.890.205522X-RAY DIFFRACTION5995
2.89-2.9160.209485X-RAY DIFFRACTION5993
2.916-2.9430.217517X-RAY DIFFRACTION5995
2.943-2.970.192487X-RAY DIFFRACTION5994
2.97-2.9990.211519X-RAY DIFFRACTION5996
2.999-3.0290.223519X-RAY DIFFRACTION5996
3.029-3.060.196506X-RAY DIFFRACTION5996
3.06-3.0930.209513X-RAY DIFFRACTION5996
3.093-3.1270.183517X-RAY DIFFRACTION5995
3.127-3.1620.196493X-RAY DIFFRACTION5994
3.162-3.20.203508X-RAY DIFFRACTION5994
3.2-3.2390.192494X-RAY DIFFRACTION5994
3.239-3.280.191503X-RAY DIFFRACTION5994
3.28-3.3230.181520X-RAY DIFFRACTION5995
3.323-3.3680.185482X-RAY DIFFRACTION5992
3.368-3.4160.187513X-RAY DIFFRACTION5995
3.416-3.4670.173512X-RAY DIFFRACTION5996
3.467-3.5210.172513X-RAY DIFFRACTION5994
3.521-3.5790.162495X-RAY DIFFRACTION5995
3.579-3.6410.172517X-RAY DIFFRACTION5996
3.641-3.7070.165522X-RAY DIFFRACTION5997
3.707-3.7780.179526X-RAY DIFFRACTION5996
3.778-3.8550.156512X-RAY DIFFRACTION5995
3.855-3.9390.157515X-RAY DIFFRACTION5995
3.939-4.030.164498X-RAY DIFFRACTION5993
4.03-4.1310.149528X-RAY DIFFRACTION5996
4.131-4.2420.154492X-RAY DIFFRACTION5995
4.242-4.3670.144531X-RAY DIFFRACTION5994
4.367-4.5080.14514X-RAY DIFFRACTION5995
4.508-4.6690.16521X-RAY DIFFRACTION5995
4.669-4.8550.16514X-RAY DIFFRACTION5994
4.855-5.0760.172506X-RAY DIFFRACTION5993
5.076-5.3420.16527X-RAY DIFFRACTION5996
5.342-5.6760.196507X-RAY DIFFRACTION5994
5.676-6.1120.215521X-RAY DIFFRACTION5994
6.112-6.7240.204534X-RAY DIFFRACTION5996
6.724-7.6890.192539X-RAY DIFFRACTION5995
7.689-9.6560.156544X-RAY DIFFRACTION5995
9.656-36.2180.18581X-RAY DIFFRACTION5996

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