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- PDB-5n6g: NerA from Agrobacterium radiobacter in complex with 2-phenylacryl... -

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Basic information

Entry
Database: PDB / ID: 5n6g
TitleNerA from Agrobacterium radiobacter in complex with 2-phenylacrylic acid
ComponentsGTN Reductase
KeywordsOXIDOREDUCTASE / Old Yellow Enzyme / Profen / ene-reductase / 2-phenylacrylic acid
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
Oxidoreductase Oye-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
2-Phenylacrylic acid / ACETATE ION / FLAVIN MONONUCLEOTIDE / GTN Reductase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsKaruppiah, V. / Toogood, H.S. / Leys, D. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I015779/1 United Kingdom
CitationJournal: Org. Biomol. Chem. / Year: 2017
Title: Structural insights into the ene-reductase synthesis of profens.
Authors: Waller, J. / Toogood, H.S. / Karuppiah, V. / Rattray, N.J.W. / Mansell, D.J. / Leys, D. / Gardiner, J.M. / Fryszkowska, A. / Ahmed, S.T. / Bandichhor, R. / Reddy, G.P. / Scrutton, N.S.
History
DepositionFeb 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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: GTN Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,92710
Polymers40,8101
Non-polymers1,1179
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-6 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.090, 69.160, 91.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTN Reductase


Mass: 40810.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: nerA / Production host: Escherichia coli (E. coli) / References: UniProt: O31246

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Non-polymers , 5 types, 396 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-8OZ / 2-Phenylacrylic acid


Mass: 148.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 47.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate, 1 M lithium chloride, 30% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.58→91.89 Å / Num. obs: 52569 / % possible obs: 99 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.042 / Net I/σ(I): 12.1
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3809 / CC1/2: 0.543 / Rpim(I) all: 0.535 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JIC

4jic


Resolution: 1.58→55.258 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.37
RfactorNum. reflection% reflection
Rfree0.1641 2671 5.09 %
Rwork0.1404 --
obs0.1416 52511 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.58→55.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 76 387 3253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082972
X-RAY DIFFRACTIONf_angle_d0.9734047
X-RAY DIFFRACTIONf_dihedral_angle_d10.0361768
X-RAY DIFFRACTIONf_chiral_restr0.062430
X-RAY DIFFRACTIONf_plane_restr0.008576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60870.31291570.2582553X-RAY DIFFRACTION98
1.6087-1.63970.23181230.23472584X-RAY DIFFRACTION98
1.6397-1.67310.23831570.21552505X-RAY DIFFRACTION98
1.6731-1.70950.24841510.20642589X-RAY DIFFRACTION98
1.7095-1.74930.20571200.18862594X-RAY DIFFRACTION99
1.7493-1.7930.20661360.1742574X-RAY DIFFRACTION98
1.793-1.84150.1821330.16342595X-RAY DIFFRACTION98
1.8415-1.89570.19681320.14982604X-RAY DIFFRACTION99
1.8957-1.95690.16561510.1382614X-RAY DIFFRACTION99
1.9569-2.02690.18421320.13092612X-RAY DIFFRACTION99
2.0269-2.1080.15731440.11752582X-RAY DIFFRACTION99
2.108-2.2040.14771520.1142629X-RAY DIFFRACTION99
2.204-2.32020.14691430.11032626X-RAY DIFFRACTION99
2.3202-2.46550.16521240.11452634X-RAY DIFFRACTION99
2.4655-2.65590.15651230.11852663X-RAY DIFFRACTION99
2.6559-2.92310.13211390.12392678X-RAY DIFFRACTION100
2.9231-3.34610.13431420.12572687X-RAY DIFFRACTION99
3.3461-4.21550.13281470.11942704X-RAY DIFFRACTION99
4.2155-55.29170.17981650.17282813X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 127.6511 Å / Origin y: 71.5159 Å / Origin z: 98.2336 Å
111213212223313233
T0.1102 Å2-0.0102 Å2-0.0018 Å2-0.1362 Å2-0.0038 Å2--0.1234 Å2
L0.6222 °2-0.0571 °2-0.091 °2-0.8973 °2-0.3343 °2--0.8136 °2
S-0.0141 Å °-0.0092 Å °-0.0445 Å °-0.0484 Å °0.0257 Å °0.0488 Å °0.1072 Å °-0.0362 Å °-0.0087 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 370)

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