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- PDB-7tnb: Caulobacter segnis arene reductase (CSAR) - WT -

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Basic information

Entry
Database: PDB / ID: 7tnb
TitleCaulobacter segnis arene reductase (CSAR) - WT
ComponentsNADH:flavin oxidoreductase/NADH oxidase
KeywordsOXIDOREDUCTASE / Reductase
Function / homologyOxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FMN binding / Aldolase-type TIM barrel / oxidoreductase activity / ACETATE ION / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase/NADH oxidase
Function and homology information
Biological speciesCaulobacter segnis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsGarfinkle, S.E. / Jeffrey, P. / Hyster, T.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127703-01 United States
CitationJournal: Nature / Year: 2022
Title: An asymmetric sp 3 -sp 3 cross-electrophile coupling using 'ene'-reductases.
Authors: Fu, H. / Cao, J. / Qiao, T. / Qi, Y. / Charnock, S.J. / Garfinkle, S. / Hyster, T.K.
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,57013
Polymers39,2051
Non-polymers1,36512
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.470, 104.175, 144.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-501-

HOH

21AAA-502-

HOH

31AAA-658-

HOH

41AAA-703-

HOH

51AAA-747-

HOH

61AAA-748-

HOH

71AAA-767-

HOH

81AAA-788-

HOH

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Components

#1: Protein NADH:flavin oxidoreductase/NADH oxidase


Mass: 39204.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter segnis (bacteria)
Strain: ATCC 21756 / DSM 7131 / JCM 7823 / NBRC 15250 / LMG 17158 / TK0059
Gene: Cseg_1902 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D5VJG6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Crystal Screen #20: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000 Protein dissolved in 100 mM KPi, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.79→29.68 Å / Num. obs: 33499 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.06 / Rrim(I) all: 0.159 / Net I/σ(I): 12.9
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 1.39 / Num. unique obs: 2315 / CC1/2: 0.745 / Rpim(I) all: 0.589 / Rrim(I) all: 1.513 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSBUILT=20180808data reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MYW

6myw


Resolution: 1.79→29.678 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.135 / SU B: 2.412 / SU ML: 0.071 / Average fsc free: 0.9395 / Average fsc work: 0.9441 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1859 1663 4.97 %
Rwork0.1531 31797 -
all0.155 --
obs-33460 99.827 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.671 Å2
Baniso -1Baniso -2Baniso -3
1--1.436 Å2-0 Å2-0 Å2
2--2.188 Å2-0 Å2
3----0.752 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 82 294 3027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152671
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.643921
X-RAY DIFFRACTIONr_angle_other_deg1.4641.5776138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0265374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06521.842152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37315429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.071522
X-RAY DIFFRACTIONr_chiral_restr0.090.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
X-RAY DIFFRACTIONr_nbd_refined0.2040.2635
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22628
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21404
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2229
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.29
X-RAY DIFFRACTIONr_nbd_other0.1650.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3290.231
X-RAY DIFFRACTIONr_mcbond_it1.341.7551446
X-RAY DIFFRACTIONr_mcbond_other1.3131.7461441
X-RAY DIFFRACTIONr_mcangle_it1.7972.6111810
X-RAY DIFFRACTIONr_mcangle_other1.7972.6131811
X-RAY DIFFRACTIONr_scbond_it2.8672.0581420
X-RAY DIFFRACTIONr_scbond_other2.7672.0161397
X-RAY DIFFRACTIONr_scangle_it4.0242.9922103
X-RAY DIFFRACTIONr_scangle_other3.9132.9292074
X-RAY DIFFRACTIONr_lrange_it5.1521.9953344
X-RAY DIFFRACTIONr_lrange_other4.95921.4883281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.8360.367920.3422315X-RAY DIFFRACTION98.0848
1.836-1.8870.3131390.2942216X-RAY DIFFRACTION99.9576
1.887-1.9410.2851240.2472208X-RAY DIFFRACTION100
1.941-2.0010.2431040.2052139X-RAY DIFFRACTION100
2.001-2.0670.1771040.1542070X-RAY DIFFRACTION100
2.067-2.1390.174980.1332032X-RAY DIFFRACTION100
2.139-2.220.185980.1271966X-RAY DIFFRACTION100
2.22-2.310.152940.1261860X-RAY DIFFRACTION100
2.31-2.4130.166830.1271814X-RAY DIFFRACTION100
2.413-2.530.18920.1211711X-RAY DIFFRACTION100
2.53-2.6670.166980.1261641X-RAY DIFFRACTION100
2.667-2.8290.176840.1231563X-RAY DIFFRACTION100
2.829-3.0240.155820.1321461X-RAY DIFFRACTION100
3.024-3.2650.156680.1281369X-RAY DIFFRACTION100
3.265-3.5760.175810.1281272X-RAY DIFFRACTION100
3.576-3.9970.129630.1221142X-RAY DIFFRACTION100
3.997-4.6130.144580.1271018X-RAY DIFFRACTION100
4.613-5.6440.174400.191890X-RAY DIFFRACTION100
5.644-7.9580.3390.226703X-RAY DIFFRACTION100
7.958-29.6780.32220.219407X-RAY DIFFRACTION97.7221

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