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

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Basic information

Entry
Database: PDB / ID: 7tmg
TitleCrystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (long b-axis)
ComponentsNAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / nitroreductase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyPutative NAD(P)H nitroreductase YdjA-like / Nitroreductase / Nitroreductase family / Nitroreductase-like / Oxidoreductases / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Putative NAD(P)H nitroreductase
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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: To be published
Title: Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (long b-axis)
Authors: Machen, A.J. / Liu, L. / Lovell, S. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
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

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Structure visualization

Structure viewerMolecule:
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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)43,8789
Polymers42,4912
Non-polymers1,3887
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-83 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.577, 99.965, 63.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-303-

PO4

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Components

#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
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.54 Å3/Da / Density % sol: 51.54 % / Mosaicity: 0.16 °
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: 1.9→46.42 Å / Num. obs: 34678 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.1 / Num. measured all: 227902 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.9-1.946.80.7961501822080.7792.499.9
9.11-46.425.80.03221593740.99943.998.5

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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: 1.9→46.42 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1663 4.8 %
Rwork0.1805 32962 -
obs0.1826 34625 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.55 Å2 / Biso mean: 30.4216 Å2 / Biso min: 16.58 Å2
Refinement stepCycle: final / Resolution: 1.9→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 87 216 3116
Biso mean--33.39 35.88 -
Num. residues----366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.960.31441410.244227132854100
1.96-2.020.26411490.225926952844100
2.02-2.090.23061650.204626982863100
2.09-2.170.23781400.186427192859100
2.17-2.270.22321130.18082751286499
2.27-2.390.23981290.18622674280398
2.39-2.540.20681480.187127342882100
2.54-2.740.21711230.19227652888100
2.74-3.020.23061280.189327682896100
3.02-3.450.24341490.19392727287699
3.45-4.350.21191290.154328252954100
4.35-46.420.20631490.16532893304298

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