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- PDB-8cqu: Flavin mononucleotide-dependent nitroreductase B.thetaiotaomicron... -

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Basic information

Entry
Database: PDB / ID: 8cqu
TitleFlavin mononucleotide-dependent nitroreductase B.thetaiotaomicron (BT_1680)
ComponentsPutative NADH dehydrogenase/NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Nitroreductase / flavin mononucleotide dependent / NADH dehydrogenase
Function / homologyNitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / CITRIC ACID / TERTIARY-BUTYL ALCOHOL / NADH dehydrogenase/NAD(P)H nitroreductase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBlaha, J. / Adam, L. / Beckham, K.S.H. / Chojnowski, G. / Wilmanns, M. / Zimmermann, M.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural insights into the diversity of nitroreductase enzymes in Bacteroides thetaiotaomicron
Authors: Blaha, J. / Adam, L. / Gratzl, S. / Chojnowski, G. / Litz, C. / Mortensen, S.A. / Zimmermann, M. / Beckham, K.S.H. / Wilmanns, M.
History
DepositionMar 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NADH dehydrogenase/NAD(P)H nitroreductase
B: Putative NADH dehydrogenase/NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7994
Polymers40,5332
Non-polymers2662
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-27 kcal/mol
Surface area15710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.009, 69.426, 47.790
Angle α, β, γ (deg.)90.000, 98.734, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 14 - 180 / Label seq-ID: 14 - 180

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Putative NADH dehydrogenase/NAD(P)H nitroreductase


Mass: 20266.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_1680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A745
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.86 Å3/Da / Density % sol: 33.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 4% t-butanol, 1.6M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976257 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976257 Å / Relative weight: 1
ReflectionResolution: 1.8→69.43 Å / Num. obs: 27611 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.07 / Rrim(I) all: 0.134 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-69.436.40.0982400.9850.0610.115
1.8-1.846.11.4916610.5721.0091.809

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSFeb 5, 2021 (BUILT 20210323)data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q8A745-F1

Resolution: 1.8→47.236 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 8.169 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1985 1340 4.857 %
Rwork0.1663 26251 -
all0.168 --
obs-27591 99.862 %
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: 35.846 Å2
Baniso -1Baniso -2Baniso -3
1--1.935 Å2-0 Å20.463 Å2
2--3.512 Å20 Å2
3----1.642 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 18 125 2766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122695
X-RAY DIFFRACTIONr_bond_other_d0.0070.0162535
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.6243636
X-RAY DIFFRACTIONr_angle_other_deg0.7311.5695915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.933512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55510505
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.59210118
X-RAY DIFFRACTIONr_chiral_restr0.0980.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023002
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02498
X-RAY DIFFRACTIONr_nbd_refined0.2140.2532
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.22354
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21306
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2116
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.214
X-RAY DIFFRACTIONr_nbd_other0.190.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.211
X-RAY DIFFRACTIONr_mcbond_it3.3792.8431338
X-RAY DIFFRACTIONr_mcbond_other3.3492.8431338
X-RAY DIFFRACTIONr_mcangle_it4.3294.2471669
X-RAY DIFFRACTIONr_mcangle_other4.3284.2491670
X-RAY DIFFRACTIONr_scbond_it5.0823.461357
X-RAY DIFFRACTIONr_scbond_other5.083.461358
X-RAY DIFFRACTIONr_scangle_it7.1774.9421967
X-RAY DIFFRACTIONr_scangle_other7.1754.9421968
X-RAY DIFFRACTIONr_lrange_it8.6343.3773005
X-RAY DIFFRACTIONr_lrange_other8.61342.5692982
X-RAY DIFFRACTIONr_ncsr_local_group_10.1490.054574
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.149490.05007
12AX-RAY DIFFRACTIONLocal ncs0.149490.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3041000.31519430.31520490.9190.89899.70720.306
1.847-1.8970.2811090.28718640.28619730.9320.9231000.272
1.897-1.9520.271830.2518230.25119060.9190.9471000.235
1.952-2.0120.2461000.23117770.23218780.9490.9699.94670.213
2.012-2.0780.272820.19817340.20118160.9420.971000.182
2.078-2.1510.221020.17516470.17817490.9720.9791000.162
2.151-2.2320.221820.16216060.16516910.9720.98299.82260.151
2.232-2.3230.277860.15915430.16516370.9580.98499.51130.15
2.323-2.4260.243870.15114960.15615840.9690.98699.93690.144
2.426-2.5440.233680.16914250.17114940.9670.98499.93310.166
2.544-2.6810.22600.17813650.1814250.9710.9831000.175
2.681-2.8430.186590.15612840.15813430.9780.9861000.161
2.843-3.0380.194460.16112200.16212680.9780.98499.84230.169
3.038-3.2810.193460.16511350.16611840.9770.98499.74660.175
3.281-3.5920.181440.15310400.15410870.980.98699.7240.171
3.592-4.0130.179510.1439440.1459950.9830.9881000.163
4.013-4.6290.146540.1248270.1258830.9890.99199.77350.146
4.629-5.6550.157430.146940.1417380.9890.99199.86450.171
5.655-7.9410.168180.1535630.1545870.9810.98898.97790.188
7.941-47.2360.185200.1813200.1813410.9860.98199.70670.2
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.41880.0728-0.18060.7050.32381.2810.0496-0.00160.00920.0140.01070.0324-0.071-0.1437-0.06030.01360.01350.01150.02910.01870.02485.9441-1.431113.9599
20.4787-0.166-0.08940.76920.19240.9579-0.00640.0125-0.1098-0.0340.0490.00990.1713-0.0666-0.04260.0481-0.01650.00590.01150.00510.068415.1577-15.10023.4425
Refinement TLS groupSelection: ALL

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