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- PDB-5j8g: Structure of nitroreductase from E. cloacae complexed with para-n... -

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Basic information

Entry
Database: PDB / ID: 5j8g
TitleStructure of nitroreductase from E. cloacae complexed with para-nitrobenzoic acid
ComponentsOxygen-insensitive NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Nitroreductase / Complex / pNBA / Substrate
Function / homology
Function and homology information


2,4,6-trinitrotoluene catabolic process / Oxidoreductases / oxidoreductase activity / cytosol
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
4-NITROBENZOIC ACID / FLAVIN MONONUCLEOTIDE / Oxygen-insensitive NAD(P)H nitroreductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHaynes, C.A. / Koder, R.L. / Miller, A.-F. / Rodgers, D.W.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS38401 United States
National Science Foundation (NSF, United States)MCB 9904886 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110787 United States
National Science Foundation (NSF, United States)IIA-1355438 United States
CitationJournal: Structure / Year: 2017
Title: Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase.
Authors: Pitsawong, W. / Haynes, C.A. / Koder, R.L. / Rodgers, D.W. / Miller, A.F.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 6, 2017Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxygen-insensitive NAD(P)H nitroreductase
B: Oxygen-insensitive NAD(P)H nitroreductase
C: Oxygen-insensitive NAD(P)H nitroreductase
D: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,89812
Polymers95,4044
Non-polymers2,4948
Water14,232790
1
A: Oxygen-insensitive NAD(P)H nitroreductase
B: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9496
Polymers47,7022
Non-polymers1,2474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-43 kcal/mol
Surface area17070 Å2
MethodPISA
2
C: Oxygen-insensitive NAD(P)H nitroreductase
D: Oxygen-insensitive NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9496
Polymers47,7022
Non-polymers1,2474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-43 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.410, 113.440, 82.290
Angle α, β, γ (deg.)90.000, 101.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxygen-insensitive NAD(P)H nitroreductase / NR


Mass: 23850.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: nfsB, nfnB, nfsI / Plasmid: PET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01234, Oxidoreductases
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-4NB / 4-NITROBENZOIC ACID / PARA NITROBENZOIC ACID


Mass: 167.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100 mM homopipes (pH 4.8), 20 mM para-nitrobenzoic acid, and 13% w/v polyethylene glycol 4000. Protein at 4.75 mg/ml initial concentration in 10 mM HEPES (pH 7.0) and 50 mM KCl

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2002 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→19.923 Å / Biso Wilson estimate: 20.01 Å2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.20.2772340.8850.1760.3231.05897.6
1.97-2.053.30.23372720.9240.1520.2791.0897.8
2.05-2.143.30.18472450.9430.1210.2211.17597.7
2.14-2.253.30.16173020.9530.1050.1931.1898.2
2.25-2.393.30.13973370.9610.0910.1671.19698.2
2.39-2.583.30.11972920.970.0780.1431.08298.4
2.58-2.843.30.10273480.9780.0660.1221.10898.7
2.84-3.253.30.08573860.9850.0560.1020.99499
3.25-4.083.20.07473900.9870.0480.0891.07698.9
4.08-203.20.06474440.990.0420.0771.05898.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.923 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 7369 10.12 %
Rwork0.1664 65425 -
obs0.1696 72794 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.22 Å2 / Biso mean: 28.6758 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: final / Resolution: 1.9→19.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 172 790 7670
Biso mean--18.91 37.46 -
Num. residues----864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037024
X-RAY DIFFRACTIONf_angle_d0.5389528
X-RAY DIFFRACTIONf_chiral_restr0.0391056
X-RAY DIFFRACTIONf_plane_restr0.0041344
X-RAY DIFFRACTIONf_dihedral_angle_d10.0364236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.26272590.19862198245797
1.9216-1.94420.21842420.17922138238098
1.9442-1.96790.2022350.17652147238298
1.9679-1.99280.20322310.17642157238898
1.9928-2.0190.19232320.16772217244998
2.019-2.04660.20972370.16952116235398
2.0466-2.07580.20042120.17052210242298
2.0758-2.10670.2182340.17132186242098
2.1067-2.13960.2062410.16572148238998
2.1396-2.17470.20962420.1672205244798
2.1747-2.21210.20552390.16862139237898
2.2121-2.25230.19392450.15812182242798
2.2523-2.29560.21512530.17072150240398
2.2956-2.34230.212390.17092198243798
2.3423-2.39320.20292560.16562173242998
2.3932-2.44880.20492410.16942150239198
2.4488-2.50990.19692280.16852229245798
2.5099-2.57760.21122450.16732161240699
2.5776-2.65330.20752520.16312193244599
2.6533-2.73870.2082590.172166242599
2.7387-2.83630.20652630.17732183244699
2.8363-2.94960.21412540.1812192244699
2.9496-3.08330.20222620.17482186244899
3.0833-3.24520.20082480.16842198244699
3.2452-3.44760.18842580.16872181243999
3.4476-3.71220.18872510.16342190244199
3.7122-4.08290.18692540.15112206246099
4.0829-4.6670.15132510.14022216246799
4.667-5.85510.17982540.15882218247299
5.8551-19.92420.22520.182192244497
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)
11.01140.1035-0.74533.6151-0.5821.36430.01710.11460.0741-0.14040.00470.1805-0.15110.00080.00280.20570.0301-0.07140.1780.02350.137929.463372.6426-43.1102
21.6771-0.76110.24114.6772-0.40482.40090.0297-0.06930.080.06990.00880.3337-0.203-0.1917-0.05250.11870.00560.02590.147-0.00570.105627.554465.347-26.4926
33.7781-0.355-0.36596.248-1.27667.4435-0.0028-0.06750.33480.0708-0.1459-0.4302-1.0520.28950.20650.4216-0.0664-0.07540.1674-0.01250.303839.738282.3825-30.6344
42.3616-0.27410.64812.3489-1.08462.57570.0833-0.2992-0.40210.3215-0.144-0.11110.13510.06740.04680.19330.01280.00140.1954-0.00030.172933.313953.2573-16.938
51.0329-0.17740.12.2725-0.62862.15390.0037-0.0350.06010.0539-0.0398-0.1112-0.18110.08350.02960.1139-0.0159-0.00820.1228-0.00080.120137.46169.9782-30.7332
61.9208-1.4349-0.04146.7347-1.37612.79430.11060.2343-0.1587-0.4528-0.271-0.12740.41110.09120.13990.2253-0.00160.01320.137-0.01660.116642.571556.3443-50.5955
70.99040.4863-0.48522.7322-0.43161.4941-0.10560.056-0.206-0.2627-0.0194-0.06350.3233-0.09190.10570.2129-0.0148-0.01490.1354-0.01920.134635.978847.2522-40.1098
85.39460.1452-0.34987.0423-0.9437.59360.14960.56550.4892-0.4042-0.5086-0.9721-0.28540.8660.37230.2519-0.06580.06910.28680.07210.280350.158167.1194-52.0247
92.8671-0.87451.85319.1286-6.71398.3311-0.7410.70230.97061.0839-0.8707-1.142-1.73162.23581.81990.7351-0.3462-0.14381.2913-0.03961.07555.445770.7301-40.5134
101.2652-0.265-0.30572.27240.33052.2077-0.01230.041-0.1351-0.0205-0.0559-0.02550.1813-0.03890.04910.1468-0.0137-0.02170.11740.02370.103236.246551.2826-33.1402
111.7162-0.1205-0.28313.29090.26110.46960.0050.1668-0.1923-0.19390.00650.00830.1274-0.0231-0.01430.13350.0006-0.02160.1709-0.0510.13051.3845-55.646-5.7249
121.23981.45221.26837.6353.4682.132-0.08530.2564-0.0345-0.56750.2979-0.4913-0.22410.3126-0.16020.0949-0.01650.04820.2175-0.00990.205816.0361-50.2754-2.1677
131.14940.20740.23063.05940.21751.00720.01070.0124-0.06490.06820.0395-0.22390.08490.1191-0.0420.06450.0092-0.00380.1427-0.00920.135114.0909-46.47169.048
142.72660.80132.73176.52020.15243.20210.3-0.0822-0.48660.1932-0.0065-0.28130.79230.4193-0.22810.25510.0245-0.05410.18770.05070.23829.8591-66.049610.9721
159.2562-0.5668-1.24738.59533.90665.71510.0698-0.7677-0.38280.7086-0.25690.88470.4904-0.13090.13740.2682-0.0720.01130.21460.07030.3223-0.4519-65.05599.6465
162.35151.3952-0.07323.42570.45331.77420.1921-0.14220.16980.34-0.0994-0.237-0.16580.2562-0.09170.0880.0244-0.01350.1687-0.00370.184919.647-41.033811.516
174.56154.39-5.94266.7882-4.13318.71180.386-0.73190.31920.544-0.3257-0.2095-0.64950.4656-0.13230.3322-0.0152-0.05160.2549-0.07740.294415.7457-29.623319.3147
181.41250.04980.05642.20970.53171.49780.0309-0.0968-0.04920.2368-0.0465-0.04530.10530.03770.01070.077-0.01170.00290.1220.00630.11777.0256-51.250311.0299
192.1808-1.23490.1844.40091.13351.32590.0840.1657-0.0697-0.171-0.12180.39150.0593-0.13940.03390.1073-0.01760.01840.18840.01490.134-9.5756-49.0425-2.4696
202.02390.62770.91975.89720.2161.4971-0.1290.30050.257-0.45380.1468-0.426-0.0830.08270.01770.1544-0.03010.05790.21350.04780.12519.1821-30.9557-5.8648
213.74844.1583-3.62684.5385-4.00713.5292-0.23930.71630.2972-0.69770.36860.30710.0809-0.4931-0.06440.1848-0.0105-0.03660.23150.01140.1894-5.9668-35.8427-6.9953
221.25070.9017-0.14565.2688-0.09960.89780.103-0.00970.24240.2152-0.07450.1076-0.165-0.0406-0.0490.07850.0160.00880.13250.00150.1582-3.7071-28.64456.3391
234.42590.5372-0.14032.47880.00395.0080.0418-0.0646-0.25940.1763-0.26140.58680.372-0.84380.06090.0993-0.05350.03790.2815-0.02410.3105-19.1291-50.28723.8199
246.11687.00375.67118.45596.6925.3331.125-0.9486-0.58631.7756-0.9549-0.06471.577-1.0098-0.17140.6857-0.14470.09710.60860.08210.559-13.5093-54.066115.3645
251.5424-0.0739-0.02433.19140.3931.86830.0122-0.0740.09410.18430.01330.0393-0.0567-0.0318-0.03780.0461-0.0038-0.00680.1209-0.00710.1237-0.2823-34.64557.4
264.31491.035-1.23394.0035-1.78655.20230.0722-0.23050.1030.2365-0.10660.3165-0.1634-0.33280.00240.0773-0.01080.01060.1159-0.04680.1395-7.1674-29.747610.0037
273.5194-2.15431.43615.3121-3.99983.9268-0.07060.33660.41790.1601-0.2735-0.6586-0.28630.30390.33830.1122-0.02010.01710.223-0.03210.187818.0139-36.78961.7946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 23 )A2 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 53 )A24 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 77 )A54 - 77
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 134 )A78 - 134
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 202 )A135 - 202
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 217 )A203 - 217
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 91 )B2 - 91
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 110 )B92 - 110
9X-RAY DIFFRACTION9chain 'B' and (resid 111 through 134 )B111 - 134
10X-RAY DIFFRACTION10chain 'B' and (resid 135 through 217 )B135 - 217
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 23 )C2 - 23
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 36 )C24 - 36
13X-RAY DIFFRACTION13chain 'C' and (resid 37 through 53 )C37 - 53
14X-RAY DIFFRACTION14chain 'C' and (resid 54 through 64 )C54 - 64
15X-RAY DIFFRACTION15chain 'C' and (resid 65 through 77 )C65 - 77
16X-RAY DIFFRACTION16chain 'C' and (resid 78 through 110 )C78 - 110
17X-RAY DIFFRACTION17chain 'C' and (resid 111 through 134 )C111 - 134
18X-RAY DIFFRACTION18chain 'C' and (resid 135 through 192 )C135 - 192
19X-RAY DIFFRACTION19chain 'C' and (resid 193 through 217 )C193 - 217
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 23 )D2 - 23
21X-RAY DIFFRACTION21chain 'D' and (resid 24 through 36 )D24 - 36
22X-RAY DIFFRACTION22chain 'D' and (resid 37 through 91 )D37 - 91
23X-RAY DIFFRACTION23chain 'D' and (resid 92 through 110 )D92 - 110
24X-RAY DIFFRACTION24chain 'D' and (resid 111 through 134 )D111 - 134
25X-RAY DIFFRACTION25chain 'D' and (resid 135 through 175 )D135 - 175
26X-RAY DIFFRACTION26chain 'D' and (resid 176 through 192 )D176 - 192
27X-RAY DIFFRACTION27chain 'D' and (resid 193 through 217 )D193 - 217

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