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- PDB-7tmf: Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneum... -

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Basic information

Entry
Database: PDB / ID: 7tmf
TitleCrystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (short b-axis)
ComponentsNAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / nitroreductase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity
Similarity search - Function
Putative NAD(P)H nitroreductase YdjA-like / : / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Putative NAD(P)H nitroreductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C 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
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 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 1.2Jul 24, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 14, 2024Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H nitroreductase
B: NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,98218
Polymers42,4912
Non-polymers2,49116
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-105 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.855, 92.216, 63.444
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NAD(P)H nitroreductase


Mass: 21245.316 Da / Num. of mol.: 2 / Fragment: KlpnC.17456.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Gene: ydjA, E3U37_20475, E3U38_02825, E9161_16570, NCTC9504_03979
Plasmid: KlpnC.17456.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A237MVZ9, Oxidoreductases

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Non-polymers , 6 types, 156 molecules

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


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.1 % / Mosaicity: 0.06 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Berkeley C1: 25 %w/v PEG 3350, 0.2 M (NH4)2SO4, 0.1 M BIS-TRIS, KlpnC.17456.a.B1.PW39057 at 21 mg/mL, Tray: plate 12177 well C1 drop 1, Puck: PSL0413, Cryo: 80% crystallant and 20% PEG 200,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→92.22 Å / Num. obs: 29253 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Net I/σ(I): 12.4 / Num. measured all: 188186 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.97-2.026.40.9621286220090.8060.4121.047299.9
9.03-92.225.90.03421713710.9970.0150.0373499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BM1

3bm1


Resolution: 1.97→55.17 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1371 4.7 %
Rwork0.1863 27820 -
obs0.1884 29191 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.55 Å2 / Biso mean: 31.4906 Å2 / Biso min: 17.91 Å2
Refinement stepCycle: final / Resolution: 1.97→55.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 149 140 3031
Biso mean--38.64 35.88 -
Num. residues----354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.040.36681590.266727052864100
2.04-2.120.27631200.218627442864100
2.12-2.220.26311440.193827312875100
2.22-2.340.25731320.198827482880100
2.34-2.480.26491350.196327572892100
2.48-2.670.25571150.191428012916100
2.67-2.940.24581270.190127692896100
2.94-3.370.25581380.195528072945100
3.37-4.240.17331640.164328052969100
4.24-55.170.21341370.17442953309099

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