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- PDB-7xww: Crystal structure of NTR in complex with BN-XB -

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Basic information

Entry
Database: PDB / ID: 7xww
TitleCrystal structure of NTR in complex with BN-XB
ComponentsDihydropteridine reductase
KeywordsFLAVOPROTEIN / reduction / fluorescence
Function / homology
Function and homology information


6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / Oxidoreductases
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-I5O / Dihydropteridine reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, X. / Chen, J. / Li, J.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 China
CitationJournal: To Be Published
Title: Crystal structure of NTR in complex with BN-XB
Authors: Chen, X. / Chen, J. / Li, J.L.
History
DepositionMay 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
B: Dihydropteridine reductase
A: Dihydropteridine reductase
H: Dihydropteridine reductase
I: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3849
Polymers96,0974
Non-polymers2,2875
Water00
1
B: Dihydropteridine reductase
A: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4225
Polymers48,0492
Non-polymers1,3743
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-49 kcal/mol
Surface area17130 Å2
MethodPISA
2
H: Dihydropteridine reductase
I: Dihydropteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9614
Polymers48,0492
Non-polymers9132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-44 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.870, 61.669, 88.332
Angle α, β, γ (deg.)96.640, 100.830, 110.720
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain H
41chain I
12chain A
22chain B
32chain H
42chain I

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPVALVALchain AAB2 - 2173 - 218
21ASPASPVALVALchain BBA2 - 2173 - 218
31ASPASPVALVALchain HHC2 - 2173 - 218
41ASPASPVALVALchain IID2 - 2173 - 218
12I5OI5OFMNFMNchain AAF - G301 - 302
22FMNFMNFMNFMNchain BBE301
32FMNFMNFMNFMNchain HHH301
42FMNFMNFMNFMNchain III301

NCS ensembles :
ID
1
2

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Components

#1: Protein
Dihydropteridine reductase / Dihydropteridine reductase / NAD(P)H-dependent / oxygen-insensitive / NAD(P)H nitroreductase / ...Dihydropteridine reductase / NAD(P)H-dependent / oxygen-insensitive / NAD(P)H nitroreductase / NAD(P)H-dependent oxidoreductase / Oxygen-insensitive NAD(P)H nitroreductase


Mass: 24024.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfnB, nfsB / Production host: Escherichia coli (E. coli)
References: UniProt: A0A094VLP5, 6,7-dihydropteridine reductase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-I5O / 2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-8-[1-[(4-nitrophenyl)methyl]pyridin-1-ium-4-yl]-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaene


Mass: 461.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24BF2N4O2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 282 K / Method: evaporation / Details: 0.04 M KH2PO4, 26% PEG8000, and 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→43.29 Å / Num. obs: 18556 / % possible obs: 90.4 % / Redundancy: 3.6 % / CC1/2: 0.963 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.089 / Rrim(I) all: 0.169 / Χ2: 0.87 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2806 / CC1/2: 0.917 / Rpim(I) all: 0.149 / Rrim(I) all: 0.285 / Χ2: 0.85 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OON

1oon


Resolution: 2.8→35.26 Å / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 44.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3786 972 5.24 %
Rwork0.2864 17570 -
obs0.2914 18542 90.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.61 Å2 / Biso mean: 39.4633 Å2 / Biso min: 4.24 Å2
Refinement stepCycle: final / Resolution: 2.8→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6726 0 124 0 6850
Biso mean--49.2 --
Num. residues----865
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2608X-RAY DIFFRACTION10.589TORSIONAL
12B2608X-RAY DIFFRACTION10.589TORSIONAL
13H2608X-RAY DIFFRACTION10.589TORSIONAL
14I2608X-RAY DIFFRACTION10.589TORSIONAL
21A28X-RAY DIFFRACTION10.589TORSIONAL
22B28X-RAY DIFFRACTION10.589TORSIONAL
23H28X-RAY DIFFRACTION10.589TORSIONAL
24I28X-RAY DIFFRACTION10.589TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8002-2.94770.42541270.3084261093
2.9477-3.13230.4571170.3268254691
3.1323-3.3740.38941400.3281240687
3.374-3.71320.43051240.3057235185
3.7132-4.24970.38731370.2741260794
4.2497-5.35120.36291610.2562256393
5.3512-35.260.29561660.2553248790
Refinement TLS params.Method: refined / Origin x: 0.6258 Å / Origin y: 18.4267 Å / Origin z: -20.9553 Å
111213212223313233
T0.0476 Å2-0.0045 Å2-0.0055 Å2-0.0663 Å2-0.0054 Å2--0.0674 Å2
L0.029 °2-0.0115 °20.0258 °2-0.0425 °20.0037 °2--0.0346 °2
S-0.0068 Å °0.0116 Å °-0.011 Å °0.0256 Å °0.003 Å °-0.052 Å °-0.0062 Å °-0.0119 Å °-0.0087 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB301 - 217
2X-RAY DIFFRACTION1allA2 - 217
3X-RAY DIFFRACTION1allC360
4X-RAY DIFFRACTION1allE361
5X-RAY DIFFRACTION1allH2 - 217
6X-RAY DIFFRACTION1allI2 - 217
7X-RAY DIFFRACTION1allJ360
8X-RAY DIFFRACTION1allL361

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