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- PDB-5ocs: Ene-reductase (ER/OYE) from Ralstonia (Cupriavidus) metallidurans -

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Basic information

Entry
Database: PDB / ID: 5ocs
TitleEne-reductase (ER/OYE) from Ralstonia (Cupriavidus) metallidurans
ComponentsPutative NADH-depentdent flavin oxidoreductase
KeywordsFLAVOPROTEIN / Old Yellow Enzyme / Ene-reductase
Function / homology
Function and homology information


: / NADPH dehydrogenase / NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
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
ACETATE ION / CITRIC ACID / FLAVIN MONONUCLEOTIDE / NADH-depentdent flavin oxidoreductase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsOpperman, D.J.
CitationJournal: Proteins / Year: 2017
Title: Structural investigation into the C-terminal extension of the ene-reductase from Ralstonia (Cupriavidus) metallidurans.
Authors: Opperman, D.J.
History
DepositionJul 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NADH-depentdent flavin oxidoreductase
B: Putative NADH-depentdent flavin oxidoreductase
C: Putative NADH-depentdent flavin oxidoreductase
D: Putative NADH-depentdent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,18110
Polymers160,7664
Non-polymers1,4156
Water21,3481185
1
D: Putative NADH-depentdent flavin oxidoreductase
hetero molecules

C: Putative NADH-depentdent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0915
Polymers80,3832
Non-polymers7083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
2
A: Putative NADH-depentdent flavin oxidoreductase
B: Putative NADH-depentdent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0915
Polymers80,3832
Non-polymers7083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-22 kcal/mol
Surface area26040 Å2
MethodPISA
3
C: Putative NADH-depentdent flavin oxidoreductase
hetero molecules

D: Putative NADH-depentdent flavin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0915
Polymers80,3832
Non-polymers7083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area5800 Å2
ΔGint-21 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.970, 95.040, 208.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative NADH-depentdent flavin oxidoreductase / Ene-reductase / Old Yellow Enzyme


Mass: 40191.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Gene: Rmet_4859 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q1LDQ5, 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1185 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium citrate tribasic pH 7, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.7→35.54 Å / Num. obs: 165966 / % possible obs: 97.4 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.039 / Rrim(I) all: 0.106 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.736.90.4860.9410.1960.52597
9.31-35.546.30.0320.9990.0140.03597.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.1data scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GR7

3gr7


Resolution: 1.7→35.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.982 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 8226 5 %RANDOM
Rwork0.1693 ---
obs0.1707 157658 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 59.01 Å2 / Biso mean: 14.154 Å2 / Biso min: 5.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2--1.16 Å20 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.7→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11288 0 96 1185 12569
Biso mean--14.74 19.94 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911721
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211083
X-RAY DIFFRACTIONr_angle_refined_deg1.61.95115976
X-RAY DIFFRACTIONr_angle_other_deg0.98325422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06651488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83623.231520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.097151774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9211594
X-RAY DIFFRACTIONr_chiral_restr0.0970.21694
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113551
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022747
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 578 -
Rwork0.21 11512 -
all-12090 -
obs--97.04 %

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