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- PDB-7s14: Crystal structure of putative NAD(P)H-flavin oxidoreductase from ... -

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Basic information

Entry
Database: PDB / ID: 7s14
TitleCrystal structure of putative NAD(P)H-flavin oxidoreductase from Haemophilus influenzae 86-028NP
ComponentsPutative NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / nitroreductase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding / metal ion binding
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
FLAVIN MONONUCLEOTIDE / : / NAD(P)H nitroreductase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsKim, Y. / Maltseva, N. / 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 Institute Of Allergy and Infectious Diseases (NIH/NIAID) 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 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 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 6, 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: Putative NAD(P)H nitroreductase
B: Putative NAD(P)H nitroreductase
C: Putative NAD(P)H nitroreductase
D: Putative NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,49619
Polymers103,1574
Non-polymers2,33815
Water6,449358
1
A: Putative NAD(P)H nitroreductase
B: Putative NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,86712
Polymers51,5792
Non-polymers1,28810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-67 kcal/mol
Surface area17550 Å2
MethodPISA
2
C: Putative NAD(P)H nitroreductase
D: Putative NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6297
Polymers51,5792
Non-polymers1,0505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-70 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.833, 54.779, 134.446
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative NAD(P)H nitroreductase / NfsB


Mass: 25789.299 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria)
Strain: 86-028NP / Gene: NTHI1892 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q4QJZ7, Oxidoreductases

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Non-polymers , 6 types, 373 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.05 Å3/Da / Density % sol: 40.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M calcium chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.621
11-h,-k,l20.379
ReflectionResolution: 1.65→50 Å / Num. obs: 97736 / % possible obs: 98.9 % / Redundancy: 4.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 4709 / CC1/2: 0.453 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19-4092refinement
PDB_EXTRACT3.27data extraction
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→42.47 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.257 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 5030 5.2 %RANDOM
Rwork0.152 ---
obs0.154 91789 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.34 Å2 / Biso mean: 29.314 Å2 / Biso min: 13.26 Å2
Baniso -1Baniso -2Baniso -3
1--5.91 Å2-0 Å2-1.42 Å2
2--2.21 Å20 Å2
3---3.7 Å2
Refinement stepCycle: final / Resolution: 1.65→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7076 0 147 358 7581
Biso mean--23.9 30.36 -
Num. residues----883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137406
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176951
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.659999
X-RAY DIFFRACTIONr_angle_other_deg1.181.58616037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03422.718401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0361548
X-RAY DIFFRACTIONr_chiral_restr0.050.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0238361
X-RAY DIFFRACTIONr_gen_planes_other0.0110.0211719
X-RAY DIFFRACTIONr_rigid_bond_restr1.1437298
LS refinement shellResolution: 1.653→1.696 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 300 -
Rwork0.193 5941 -
all-6241 -
obs--85.6 %
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)
11.1163-1.30130.43381.5605-0.32940.89460.0132-0.01520.03090.00750.0152-0.04620.0671-0.0473-0.02840.06950.00210.01220.04930.00990.04677.313611.220666.4874
20.01480.0065-0.00230.00770.00330.00420.0103-0.0273-0.0078-0.0176-0.0128-0.0041-0.02030.00190.00250.109-0.01140.01240.05930.00560.028713.767613.866648.667
31.1179-0.52920.51470.3631-0.35210.3429-0.15130.05320.1208-0.02650.0226-0.14030.03-0.02680.12870.1225-0.04350.04630.0989-0.01110.086615.704714.05636.5216
44.81061.61910.78891.45322.06893.7188-0.03750.16270.1403-0.15320.0220.0524-0.2702-0.01990.01550.10640.0153-0.00570.032-0.00440.03454.155210.798632.0144
50.3973-0.02660.40681.525-0.09130.4205-0.0531-0.00670.0370.04060.0091-0.121-0.0452-0.00240.0440.09790.00610.03440.03740.00190.032212.213611.373239.5436
61.3892-1.36951.82732.1115-2.78763.6901-0.17430.00050.08190.0687-0.0686-0.1811-0.12440.08320.24290.15140.00950.01670.0532-0.01740.03831.6765-5.788345.0501
73.0779-0.82050.2470.4789-0.46530.63630.1113-0.08770.1836-0.0281-0.0635-0.0132-0.00740.1137-0.04780.11680.00620.02290.0528-0.00660.021328.2071-14.651448.2914
80.391-0.19890.020.1031-0.0310.3612-0.0088-0.00070.00190.01080.00060.00030.0167-0.01440.00820.0786-0.01160.0190.0269-0.0020.023112.36943.138945.6838
91.1245-0.4991-0.70290.22210.31230.4448-0.01070.1984-0.120.0035-0.07570.04980.0337-0.11150.08650.1509-0.00510.05670.1602-0.01430.062617.66284.421429.5853
101.4645-2.0929-1.12883.08861.78241.16660.06310.0179-0.0313-0.1276-0.04960.0251-0.1295-0.0543-0.01360.08820.00090.02670.03090.01250.019813.27017.09140.9179
110.24010.07970.01681.9361-0.98530.5190.060.0541-0.0007-0.0427-0.03490.04870.02950.0443-0.02510.0942-0.00440.0320.06010.00140.0192-1.56593.718457.3993
121.43661.17970.17140.96890.14070.0205-0.00680.0073-0-0.00290.0069-0.00060.00030.0023-0.00010.12820.02650.02330.08390.0170.017814.283717.866161.6423
130.03410.0045-0.03020.0013-0.00340.0319-0.01880.0018-0.0274-0.0001-0.0029-0.00770.03660.00320.02170.09780.00720.01290.04130.00980.05211.3578-0.869264.9408
140.5176-0.23960.25360.1258-0.21120.72320.0064-0.0118-0.0107-0.01310.01130.00870.0659-0.0407-0.01770.0766-0.01260.0190.0314-0.00190.02213.5194-13.646664.2927
150.79810.3076-0.12880.1247-0.07040.10660.0009-0.0034-0.02780.0213-0.01-0.0046-0.06550.02280.00920.1243-0.00280.02410.0507-0.02220.0459-5.0906-4.850240.8733
160.2033-0.0176-0.00320.0136-0.02930.0733-0.00420.0086-0.0417-0.001-0.00280.00110.00290.01180.0070.0913-0.00130.01340.033-0.00460.02310.8159-9.815555.81
171.11310.3482-0.45121.1091-1.86253.14580.01320.0053-0.02850.1435-0.0841-0.0419-0.24470.14840.07090.14050.00180.02010.00950.00660.010626.29556.95454.0825
180.16590.0844-0.43660.37420.53592.88390.0625-0.01670.02730.02430.01290.0097-0.17810.0916-0.07540.10710.0040.0150.0328-0.00540.0409-20.2572-35.99610.3698
191.49290.04190.16781.01440.03920.02010.0916-0.045-0.23620.0751-0.0670.00450.0134-0.0079-0.02460.0934-0.00750.00920.0558-0.00130.0449-14.4553-39.069318.0856
202.69682.6817-2.31023.0197-1.76133.04560.0621-0.1063-0.13910.1213-0.0684-0.1259-0.03460.01740.00630.06770.01830.03590.0920.07050.0818-14.2281-39.566931.8045
212.4391-1.1190.12750.5157-0.05930.0114-0.1828-0.5047-0.51630.08780.21790.2281-0.0345-0.011-0.03520.1656-0.04250.03680.17230.12150.1486-19.745-36.446729.4602
220.9076-0.08860.81390.9447-0.2660.76870.053-0.0377-0.0279-0.0153-0.01150.09570.0626-0.0303-0.04150.0817-0.00560.02160.03450.01970.0313.2276-19.593222.4603
233.20151.0651-0.99050.358-0.30440.48550.0801-0.1590.00560.0319-0.0559-0.00290.0310.0381-0.02420.07830.00240.03610.0331-0.01440.0729-0.2588-10.607919.4323
241.30260.2910.38820.51790.1890.14020.0161-0.0508-0.05490.041-0.00950.01150.0116-0.0213-0.00660.0722-0.00230.02020.0442-0.00470.0294-15.9988-28.500821.4133
254.5712-1.4844-0.30784.2183-2.09281.3076-0.2075-0.6263-0.21730.0840.25270.16880.00210.0127-0.04520.1285-0.01710.02810.10440.02570.0197-10.5613-30.34937.5107
260.89530.00240.20470.01270.00010.04690.0287-0.0668-0.05810.0228-0.01510.00370.0038-0.0159-0.01360.09670.00530.01690.04570.00670.0077-26.0477-29.87514.0024
273.7081-1.9904-0.16332.1811.52341.8607-0.0195-0.0876-0.20340.07780.04830.07880.07660.0029-0.02890.1397-0.01180.01290.12590.02880.0417-13.377-42.37055.2014
280.60660.1723-0.09180.1781-0.10110.06030.0170.03460.0212-0.0033-0.0181-0.01-0.0130.00810.00110.09380.00470.02350.02970.00090.0333-16.0416-16.88732.9574
290.73820.4022-0.55871.6206-1.22271.02750.0076-0.02860.04-0.1441-0.0211-0.04730.07630.02950.01350.0974-0.01080.01830.0524-0.00980.008-35.4525-19.087221.6369
300.5232-0.06380.20350.0158-0.02190.0811-0.0136-0.09660.01590.02460.0020.00450.008-0.03850.01160.0962-0.00680.02980.0426-0.00740.0275-25.1159-21.803422.7849
310.3480.4235-0.03520.5195-0.04510.00480.0159-0.01390.02580.0209-0.02090.017-0.0010.00370.0050.09060.00320.01540.05770.00190.0586-17.1102-10.61899.4522
323.0433-0.35270.21930.054-0.02940.0175-0.00790.3279-0.4780.0062-0.01270.00110.00480.0250.02060.1373-0.03890.04870.0672-0.0180.3166-1.724-31.69512.3976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 15
2X-RAY DIFFRACTION2A16 - 51
3X-RAY DIFFRACTION3A52 - 64
4X-RAY DIFFRACTION4A65 - 75
5X-RAY DIFFRACTION5A76 - 89
6X-RAY DIFFRACTION6A90 - 109
7X-RAY DIFFRACTION7A110 - 133
8X-RAY DIFFRACTION8A134 - 171
9X-RAY DIFFRACTION9A172 - 188
10X-RAY DIFFRACTION10A189 - 198
11X-RAY DIFFRACTION11A199 - 220
12X-RAY DIFFRACTION12B-2 - 14
13X-RAY DIFFRACTION13B15 - 51
14X-RAY DIFFRACTION14B52 - 89
15X-RAY DIFFRACTION15B90 - 133
16X-RAY DIFFRACTION16B134 - 198
17X-RAY DIFFRACTION17B199 - 220
18X-RAY DIFFRACTION18C1 - 15
19X-RAY DIFFRACTION19C16 - 51
20X-RAY DIFFRACTION20C52 - 67
21X-RAY DIFFRACTION21C68 - 89
22X-RAY DIFFRACTION22C90 - 109
23X-RAY DIFFRACTION23C110 - 133
24X-RAY DIFFRACTION24C134 - 171
25X-RAY DIFFRACTION25C172 - 188
26X-RAY DIFFRACTION26C189 - 220
27X-RAY DIFFRACTION27D-1 - 14
28X-RAY DIFFRACTION28D15 - 89
29X-RAY DIFFRACTION29D90 - 109
30X-RAY DIFFRACTION30D110 - 159
31X-RAY DIFFRACTION31D160 - 198
32X-RAY DIFFRACTION32D199 - 219

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