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- PDB-8dor: Crystal structure of Dihydropteridine reductase/oxygen-insensitiv... -

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Basic information

Entry
Database: PDB / ID: 8dor
TitleCrystal structure of Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase from Klebsiella pneumoniae
ComponentsDihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystal structures of NAD(P)H nitroreductases from Klebsiella pneumoniae.
Authors: Kancherla, A.D. / Liu, L. / Tillery, L. / Shek, R. / Craig, J.K. / Machen, A.J. / Seibold, S. / Battaile, K.P. / Fradi, S. / Barrett, L.K. / Subramanian, S. / Myler, P. / Van Voorhis, W.C. / Lovell, S.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.3Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
B: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
C: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
D: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,96322
Polymers99,8374
Non-polymers3,12618
Water19,4021077
1
A: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
B: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,48111
Polymers49,9182
Non-polymers1,5639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-71 kcal/mol
Surface area16590 Å2
MethodPISA
2
C: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
D: Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,48111
Polymers49,9182
Non-polymers1,5639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-68 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.826, 56.826, 257.568
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 24959.158 Da / Num. of mol.: 4 / Fragment: KlpnC.20499.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: nfnB, KPN_00553, KPHS_29700 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6T5Y2
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1077 / 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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: JCSG+ D12: 16% (w/v) PEG 8000; 20% (v/v) glycerol, 0.04 M K2HPO4, KlpnC.20499.a.B1.PW39082 at 30 mg/mL, Tray: plate 12477 well D12 drop 2, Puck: PSL1107, Cryo: DIRECT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 24, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.35→49.21 Å / Num. obs: 204417 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.032 / Rrim(I) all: 0.106 / Net I/σ(I): 13.5 / Num. measured all: 2214463 / Scaling rejects: 56
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.35-1.3910.51.14160267152060.7640.3621.1972.1
6.04-49.21120.02727682231510.0080.02849.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ICR

1icr


Resolution: 1.35→29.47 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 16.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1617 10395 5.09 %
Rwork0.1332 193819 -
obs0.1346 204214 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.34 Å2 / Biso mean: 16.6858 Å2 / Biso min: 6.84 Å2
Refinement stepCycle: final / Resolution: 1.35→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 204 1077 7983
Biso mean--21.37 27.18 -
Num. residues----866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.35-1.370.24413560.189864406796
1.37-1.380.2253570.179564346791
1.38-1.40.24023200.17364016721
1.4-1.420.22213740.165965026876
1.42-1.430.21553460.159464416787
1.43-1.450.20623840.157264796863
1.45-1.480.19773860.148364056791
1.48-1.50.19063650.143964826847
1.5-1.520.19762760.128864566732
1.52-1.550.17893240.131465296853
1.55-1.570.15223400.121364466786
1.57-1.60.16994080.121163916799
1.6-1.630.1623420.118264986840
1.63-1.660.16913340.118264636797
1.66-1.70.16973140.117364396753
1.7-1.740.16943260.119664266752
1.74-1.780.15183170.121365986915
1.78-1.830.15073790.125464986877
1.83-1.890.15593520.131363816733
1.89-1.950.16593420.125564126754
1.95-2.020.15493460.126665086854
2.02-2.10.14933100.125365566866
2.1-2.190.15683400.125864796819
2.19-2.310.16583320.131664036735
2.31-2.450.15383420.135465196861
2.45-2.640.16533280.141764206748
2.64-2.910.16383920.139764436835
2.91-3.330.15983690.1464626831
3.33-4.190.1453410.127864536794
4.19-29.470.13233530.129364556808

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