[English] 日本語
Yorodumi
- PDB-5j8g: Structure of nitroreductase from E. cloacae complexed with para-n... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more