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- PDB-7rzl: Crystal structure of putative NAD(P)H-flavin oxidoreductase from ... -

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Basic information

Entry
Database: PDB / ID: 7rzl
TitleCrystal structure of putative NAD(P)H-flavin oxidoreductase from Haemophilus influenzae R2846 in complex with 4-nitrophenol
Components(NAD(P)H-dependent ...) x 2
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyOxygen-insensitive NAD(P)H nitroreductase NfsB-like / Nitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / FORMIC ACID / P-NITROPHENOL / NAD(P)H-dependent oxidoreductase
Function and homology information
Biological speciesHaemophilus influenzae R2846 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsMaltseva, N. / Kim, Y. / Endres, M. / Crofts, T. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Microbiol Spectr / Year: 2022
Title: Functional and Structural Characterization of Diverse NfsB Chloramphenicol Reductase Enzymes from Human Pathogens.
Authors: Mullowney, M.W. / Maltseva, N.I. / Endres, M. / Kim, Y. / Joachimiak, A. / Crofts, T.S.
History
DepositionAug 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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: NAD(P)H-dependent oxidoreductase
B: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,50810
Polymers51,9092
Non-polymers1,5998
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-32 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.712, 77.700, 90.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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NAD(P)H-dependent ... , 2 types, 2 molecules AB

#1: Protein NAD(P)H-dependent oxidoreductase


Mass: 25946.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae R2846 (bacteria)
Gene: CH638_05260 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: A0A3E1QXW7, NAD(P)H dehydrogenase (quinone)
#2: Protein NAD(P)H-dependent oxidoreductase


Mass: 25962.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae R2846 (bacteria)
Gene: CH638_05260 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: A0A3E1QXW7, NAD(P)H dehydrogenase (quinone)

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Non-polymers , 6 types, 271 molecules

#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: 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
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 1.88 Å3/Da / Density % sol: 34.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M magnesium chloride, 0.1 M HEPES, pH 7.5, 30% PEG550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 23, 2021
RadiationMonochromator: dauble crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 68981 / % possible obs: 99.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 12.15 Å2 / CC1/2: 0.998 / Net I/σ(I): 25.8
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3288 / CC1/2: 0.547

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→40.11 Å / SU ML: 0.1127 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.3529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1902 3183 4.95 %
Rwork0.1475 61175 -
obs0.1496 68981 92.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.27 Å2
Refinement stepCycle: LAST / Resolution: 1.45→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3542 0 108 263 3913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754102
X-RAY DIFFRACTIONf_angle_d1.02645566
X-RAY DIFFRACTIONf_chiral_restr0.0851570
X-RAY DIFFRACTIONf_plane_restr0.009730
X-RAY DIFFRACTIONf_dihedral_angle_d11.5161630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.2213410.1574891X-RAY DIFFRACTION31.31
1.47-1.490.2135750.161340X-RAY DIFFRACTION47.63
1.49-1.520.23281080.15082008X-RAY DIFFRACTION71.95
1.52-1.540.20051270.14632540X-RAY DIFFRACTION89.62
1.54-1.570.20971360.13742773X-RAY DIFFRACTION97.78
1.57-1.60.19381680.12592799X-RAY DIFFRACTION99.4
1.6-1.640.18161380.11882853X-RAY DIFFRACTION99.77
1.64-1.670.18151530.12022796X-RAY DIFFRACTION99.9
1.67-1.710.16281460.12412849X-RAY DIFFRACTION99.93
1.71-1.750.16441410.12812829X-RAY DIFFRACTION100
1.75-1.80.18871440.13082859X-RAY DIFFRACTION100
1.8-1.850.19331420.12552829X-RAY DIFFRACTION99.97
1.85-1.910.17621740.13072823X-RAY DIFFRACTION99.97
1.91-1.980.21371500.12572837X-RAY DIFFRACTION99.9
1.98-2.060.17291390.13212863X-RAY DIFFRACTION99.8
2.06-2.150.17111500.13242867X-RAY DIFFRACTION100
2.15-2.270.18451420.13192867X-RAY DIFFRACTION99.93
2.27-2.410.17721280.14492869X-RAY DIFFRACTION100
2.41-2.60.18381480.16092905X-RAY DIFFRACTION99.84
2.6-2.860.21871680.1682861X-RAY DIFFRACTION99.8
2.86-3.270.19071490.1662905X-RAY DIFFRACTION100
3.27-4.120.18661500.14462951X-RAY DIFFRACTION99.9
4.12-40.110.19771660.17723061X-RAY DIFFRACTION99.81

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