[English] 日本語
Yorodumi
- PDB-5a4k: Crystal structure of the R139W variant of human NAD(P)H:quinone o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5a4k
TitleCrystal structure of the R139W variant of human NAD(P)H:quinone oxidoreductase
ComponentsNAD(P)H DEHYDROGENASE [QUINONE] 1
KeywordsOXIDOREDUCTASE / NQO1 / FAD / FLAVOPROTEIN / OXIDATIVE STRESS / QUINONE REDUCTASE / DRUG METABOLISM / SINGLE AMINO ACID EXCHANGE
Function / homology
Function and homology information


response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion ...response to L-glutamine / response to flavonoid / ubiquinone metabolic process / response to hydrogen sulfide / vitamin E metabolic process / vitamin K metabolic process / NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH oxidation / cellular response to metal ion / cytochrome-b5 reductase activity, acting on NAD(P)H / NADPH oxidation / response to tetrachloromethane / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / synaptic transmission, cholinergic / response to alkaloid / response to carbohydrate / Regulation of ornithine decarboxylase (ODC) / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to testosterone / response to amine / superoxide dismutase activity / response to electrical stimulus / nitric oxide biosynthetic process / xenobiotic metabolic process / removal of superoxide radicals / response to hormone / response to nutrient / cell redox homeostasis / response to ischemia / protein catabolic process / negative regulation of protein catabolic process / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of neuron apoptotic process / response to estradiol / cellular response to oxidative stress / response to ethanol / response to oxidative stress / response to lipopolysaccharide / innate immune response / dendrite / neuronal cell body / synapse / negative regulation of apoptotic process / RNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NAD(P)H dehydrogenase [quinone] 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.093 Å
AuthorsLienhart, W.D. / Strandback, E. / Gudipati, V. / Uhl, M.K. / Rantase, D.M. / Zangger, K. / Gruber, K. / Macheroux, P.
CitationJournal: FEBS J. / Year: 2017
Title: Catalytic competence, structure and stability of the cancer-associated R139W variant of the human NAD(P)H:quinone oxidoreductase 1 (NQO1).
Authors: Lienhart, W.D. / Strandback, E. / Gudipati, V. / Koch, K. / Binter, A. / Uhl, M.K. / Rantasa, D.M. / Bourgeois, B. / Madl, T. / Zangger, K. / Gruber, K. / Macheroux, P.
History
DepositionJun 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
B: NAD(P)H DEHYDROGENASE [QUINONE] 1
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
D: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,99310
Polymers132,4324
Non-polymers3,5616
Water18,9521052
1
B: NAD(P)H DEHYDROGENASE [QUINONE] 1
C: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9965
Polymers66,2162
Non-polymers1,7803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-50 kcal/mol
Surface area21510 Å2
MethodPISA
2
A: NAD(P)H DEHYDROGENASE [QUINONE] 1
D: NAD(P)H DEHYDROGENASE [QUINONE] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9965
Polymers66,2162
Non-polymers1,7803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-49.8 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.606, 56.928, 99.827
Angle α, β, γ (deg.)100.37, 92.85, 90.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.993274, 0.05409, 0.102374), (0.050005, -0.597062, 0.800635), (0.10443, 0.800369, 0.590342)16.719, 17.47, -9.931
2given(-0.992907, -0.056015, -0.104869), (-0.050851, -0.597219, 0.800464), (-0.107468, 0.800119, 0.590135)31.852, 35.016, -15.518

-
Components

#1: Protein
NAD(P)H DEHYDROGENASE [QUINONE] 1 / AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NAD(P)H\:QUINONE OXIDOREDUCTASE 1 / ...AZOREDUCTASE / DT-DIAPHORASE / DTD / MENADIONE REDUCTASE / NAD(P)H\:QUINONE OXIDOREDUCTASE 1 / PHYLLOQUINONE REDUCTASE / QUINONE REDUCTASE 1 / QR1 / NADPH QUINONE OXIDOREDUCTASE


Mass: 33107.984 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P15559, NAD(P)H dehydrogenase (quinone)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1052 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS-TAG AND CLEAVAGE SITE R139W VARIANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.57 % / Description: NONE
Crystal growDetails: 200 MM LI2SO4, 100 MM BISTRIS (PH 6.5), 25% W/V PEG 3350, PROTEIN CONCENTRATION: 6.1 MG/ML

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Details: TOROIDAL FOCUSING
RadiationMonochromator: BARTELS MONOCHROMATOR, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→49.03 Å / Num. obs: 67587 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.27
Reflection shellResolution: 2.09→2.17 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 86.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBG

1qbg


Resolution: 2.093→49.033 Å / SU ML: 0.22 / σ(F): 1.97 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 3418 5.1 %
Rwork0.1693 --
obs0.1709 67536 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.093→49.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8644 0 240 1052 9936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039160
X-RAY DIFFRACTIONf_angle_d0.95112429
X-RAY DIFFRACTIONf_dihedral_angle_d15.8983333
X-RAY DIFFRACTIONf_chiral_restr0.1041299
X-RAY DIFFRACTIONf_plane_restr0.0031545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0932-2.12310.3198950.26212016X-RAY DIFFRACTION73
2.1231-2.15480.2391510.2152646X-RAY DIFFRACTION97
2.1548-2.18850.25321660.20862724X-RAY DIFFRACTION97
2.1885-2.22430.2981410.2072584X-RAY DIFFRACTION97
2.2243-2.26270.25831360.22735X-RAY DIFFRACTION97
2.2627-2.30380.21941390.19712648X-RAY DIFFRACTION97
2.3038-2.34810.2351660.18652664X-RAY DIFFRACTION97
2.3481-2.39610.22551340.18392697X-RAY DIFFRACTION97
2.3961-2.44820.21761170.17772697X-RAY DIFFRACTION98
2.4482-2.50510.23431410.18522694X-RAY DIFFRACTION98
2.5051-2.56780.20991380.17192752X-RAY DIFFRACTION98
2.5678-2.63720.19721440.18082700X-RAY DIFFRACTION98
2.6372-2.71480.19921310.18152726X-RAY DIFFRACTION98
2.7148-2.80240.23371500.17782679X-RAY DIFFRACTION98
2.8024-2.90250.24251500.18852689X-RAY DIFFRACTION98
2.9025-3.01870.21151760.17882709X-RAY DIFFRACTION98
3.0187-3.15610.19081350.17332706X-RAY DIFFRACTION98
3.1561-3.32250.18561530.1722706X-RAY DIFFRACTION99
3.3225-3.53060.18581250.15122722X-RAY DIFFRACTION99
3.5306-3.80310.17711340.14442737X-RAY DIFFRACTION99
3.8031-4.18560.17591330.13912727X-RAY DIFFRACTION99
4.1856-4.79080.14431500.12972703X-RAY DIFFRACTION99
4.7908-6.03420.17021640.14882741X-RAY DIFFRACTION99
6.0342-49.04640.18041490.16942716X-RAY DIFFRACTION99
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)
11.1215-0.09140.08310.83340.2731.4014-0.0378-0.1369-0.07110.0848-0.02280.10280.122-0.25420.03780.1415-0.01930.02080.191400.15050.661820.478833.1882
21.8523-0.24540.39691.05890.76791.4266-0.1863-0.40460.3470.1855-0.01040.0978-0.2632-0.39780.19660.28280.0527-0.01650.3764-0.08570.22540.508240.509648.274
30.93780.1715-0.07170.5870.14091.4466-0.01910.1720.1269-0.0745-0.01750.0742-0.11-0.26530.02620.15190.0323-0.0140.1960.00510.16585.868823.6081-10.494
41.56160.1478-0.33610.60420.57151.2073-0.08950.4333-0.3099-0.1649-0.09930.10590.2918-0.27240.17080.276-0.06360.010.3743-0.10280.21115.7833.581-25.4278
50.9853-0.0902-0.03831.35080.14510.93460.0002-0.03080.02550.07570.0097-0.1456-0.07170.0736-0.00940.1501-0.0085-0.00030.1106-0.00180.155226.861118.17581.1224
61.14750.01720.07370.88380.05111.263-0.06080.2227-0.1178-0.13080.0091-0.12350.06210.08920.04420.1732-0.00910.03370.1736-0.04670.179225.80416.9633-15.8221
70.89360.02560.10141.39610.22650.8166-0.00550.0312-0.0512-0.04310.0276-0.10950.05280.0826-0.00130.13230.01810.00290.09580.01020.127521.635925.880221.627
81.1195-0.0156-0.03960.99680.04391.1242-0.0303-0.1870.1090.13840.0186-0.0994-0.05280.08320.00510.1760.016-0.02040.1728-0.03890.163220.535137.021638.6394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:223)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 224:274)
3X-RAY DIFFRACTION3(CHAIN B AND RESID 3:223)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 224:274)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 3:128)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 129:273)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 3:128)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 129:272)

+
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://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