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

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Basic information

Entry
Database: PDB / ID: 7rzp
TitleCrystal structure of putative NAD(P)H-flavin oxidoreductase from Haemophilus influenzae R2866
ComponentsDihydropteridine reductase, NAD(P)H-dependent, oxygen-insensitive
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN MONONUCLEOTIDE / NAD(P)H-dependent oxidoreductase
Similarity search - Component
Biological speciesHaemophilus influenzae R2866 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropteridine reductase, NAD(P)H-dependent, oxygen-insensitive
B: Dihydropteridine reductase, NAD(P)H-dependent, oxygen-insensitive
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9249
Polymers51,6712
Non-polymers1,2537
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-55 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.170, 56.170, 122.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 25835.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae R2866 (bacteria)
Gene: CH609_03695, NCTC11873_01313 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A3E1R3Y4, FMN reductase (NADPH)

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Non-polymers , 5 types, 178 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium acetate; 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 15, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 31406 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 29.71 Å2 / CC1/2: 0.978 / Net I/σ(I): 13.5
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 1548 / CC1/2: 0.361

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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: 1.95→48.64 Å / SU ML: 0.245 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.0937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 1620 5.19 %
Rwork0.1708 29597 -
obs0.1733 31217 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 83 171 3789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01063724
X-RAY DIFFRACTIONf_angle_d1.19685030
X-RAY DIFFRACTIONf_chiral_restr0.0617535
X-RAY DIFFRACTIONf_plane_restr0.0125638
X-RAY DIFFRACTIONf_dihedral_angle_d9.8266511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.33741230.26422401X-RAY DIFFRACTION96.01
2.01-2.070.30561400.23262447X-RAY DIFFRACTION98.67
2.07-2.150.27031160.2142437X-RAY DIFFRACTION99.3
2.15-2.230.24571180.1752507X-RAY DIFFRACTION99.85
2.24-2.340.24211540.2182480X-RAY DIFFRACTION100
2.34-2.460.25341080.21632471X-RAY DIFFRACTION100
2.46-2.610.2711060.20442517X-RAY DIFFRACTION100
2.61-2.820.22851560.18212503X-RAY DIFFRACTION100
2.82-3.10.23111580.1892445X-RAY DIFFRACTION100
3.1-3.550.20561200.16122482X-RAY DIFFRACTION100
3.55-4.470.1791500.12962468X-RAY DIFFRACTION100
4.47-48.640.18421710.13712439X-RAY DIFFRACTION99.89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.614239971851.741264635111.168984576486.10601570612-0.1198794358836.218257391860.0760734772450.8665464460190.143712664319-0.492546520266-0.0003538959724930.193718984298-0.511549020342-0.4881801319270.007419872897460.2411878800870.03072792429-0.04605884669350.5291224775840.0482045997070.24812586622811.543230231235.1535384297-5.72919356722
27.30806371875-1.46114145925-0.5187623418882.62840624112-0.5306091627181.03645404771-0.108613101677-0.00627674016039-0.175156412936-0.1887150324450.2459511392150.5018113783910.0191699772087-0.499475305705-0.1140641510790.23056869950.0302965416852-0.03835220345940.340936850790.05603185979280.2216637211138.3536122411626.451367518310.317911595
32.424526457231.02967527354-0.7196506321233.01003069854-0.2808683921532.87040849647-0.00379175600099-0.3733029621490.1595023734860.4001618442780.1613501227070.549993420627-0.116928143594-0.446602726659-0.1468280577120.2495556502490.06613100973050.06429081450920.3534608307540.06522504511150.2797077385044.6695951380528.294861374524.3082823086
43.340419116390.140319454706-0.08653237051791.63567100282-0.6069631982952.02261051808-0.137975080554-0.121453013013-0.1716594331440.09028062778190.0273928163804-0.1501353565750.02417007461590.1036446054710.09541604703740.1975812881440.05160301604760.01196638320320.1474297629460.01522008157950.17382561394725.966127559127.532802250917.8851626441
53.975119518030.28134736144-0.2499976193932.18373067427-0.6844411725482.24578463605-0.0851150037212-0.2572613848860.01204481215350.30232187080.1186975417770.249843172517-0.0855328855134-0.18911522855-0.05081030232960.2598452828730.07327099735950.05180592760350.2437471856830.01892601299980.22745101562911.239251865629.182637171324.2146490664
61.520743120432.038166575760.01069777972363.69007347145-1.225960454971.728474662510.06167864285590.2231400351190.754357754323-0.1346579484130.2448112124390.769616565509-0.481117038893-0.42395919548-0.2385165829310.3767236807830.0821269258110.04456427301350.3671063142930.1459191312740.51763725053911.810730067146.39435440583.75557395481
76.957707359140.7421007912562.315212801573.31883648171-0.0544900424125.631492997880.3950611387680.39965655691-0.0749676091197-0.4246958566160.05881348866940.06561457558060.573481883679-0.238771445646-0.4054035452610.433773066473-0.0652020664839-0.0438479142930.410082660414-0.01339010675320.25718713756110.333896933125.1532372375-2.16140892195
83.71632484345-1.73302576095-3.238108808961.332181727651.036367219295.362175081790.2199000490870.3420800469920.293551090369-0.09397147404930.0197635286166-0.0808827873155-0.206443364263-0.32467531775-0.2282086895660.2351286211490.000656550991109-0.009669054281930.2178897874940.03215192544250.21488472454922.874608555438.9014317613-1.26105564764
94.962164594750.781466592628-0.5755250518753.38066995343-0.6005198681324.866923908680.003513920820010.4499727648690.0597030568344-0.2488169613690.00529407946369-0.595135258394-0.196271576420.779160803994-0.03537148030730.240145985504-0.04337051056810.04721280630920.3217946428540.03309855494510.28972872041636.450770337441.44585403241.66265153644
101.93703801935-0.201885548302-0.8538996141241.94850747053-0.008015885835411.805302507780.1001606576-0.06729213616110.4246087220840.2931200590560.06718055426940.142413163119-0.37599753948-0.137953754399-0.08070062930220.2843158669220.06107399078020.03137197394410.1613716026040.0232583919950.28728023752218.767508325245.032542877116.241533862
115.221543222870.9094579763440.8755670327155.338182318760.1054252229845.120126204940.111191928151-0.1503628664350.9735783019290.3195160209140.230425172488-0.800552577375-0.8579000288420.569220590897-0.2167570159420.42388113462-0.1400184755140.02003367009640.2507952070070.02882660283840.56125789445335.609953466250.91178719511.6379685352
122.816034934880.857860637735-2.076065301221.14451400138-1.090283630892.90437628455-0.2669314138670.319594405046-0.411204683878-0.1845949164850.00664418321121-0.2068109310810.365987251734-0.1896189112370.2801240491770.2375926597870.0424855680989-0.02889598211160.243331378180.003714799360060.22462819807323.039152624525.69577369436.87455194017
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 15 )AA1 - 151 - 15
22chain 'A' and (resid 16 through 51 )AA16 - 5116 - 51
33chain 'A' and (resid 52 through 74 )AA52 - 7452 - 74
44chain 'A' and (resid 75 through 158 )AA75 - 15875 - 158
55chain 'A' and (resid 159 through 198 )AA159 - 198159 - 198
66chain 'A' and (resid 199 through 220 )AA199 - 220199 - 220
77chain 'B' and (resid 1 through 15 )BF1 - 151 - 15
88chain 'B' and (resid 16 through 51 )BF16 - 5116 - 51
99chain 'B' and (resid 52 through 81 )BF52 - 8152 - 81
1010chain 'B' and (resid 82 through 171 )BF82 - 17182 - 171
1111chain 'B' and (resid 172 through 188 )BF172 - 188172 - 188
1212chain 'B' and (resid 189 through 220 )BF189 - 220189 - 220

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