[English] 日本語
Yorodumi
- PDB-8bpp: crystal structure of N-ethylmaleimide reductase (nemA) from Esche... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bpp
Titlecrystal structure of N-ethylmaleimide reductase (nemA) from Escherichia coli
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / old yellow enzyme / OYE / E. coli / maleimide
Function / homology
Function and homology information


N-ethylmaleimide reductase activity / oxidoreductase activity, acting on other nitrogenous compounds as donors, with NAD or NADP as acceptor / nitroglycerin metabolic process / 2,4,6-trinitrotoluene catabolic process / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / xenobiotic metabolic process / FMN binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPfister, P. / Tinzl, M. / Erb, T.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
Max Planck Society190003 Germany
European Research Council (ERC)637675European Union
CitationJournal: To Be Published
Title: Development of the Biocatalytic Reductive Aldol Reaction
Authors: Tinzl, M. / Stoffel, G.M.M. / Saez, D.A. / Gerlinger, P.D. / Recabarren, R. / Bradley, T. / Westedt, H. / Pfister, P. / Gomez, A. / Ebert, M.O. / Voehringer-Martinez, E. / Erb, T.J.
History
DepositionNov 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-ethylmaleimide reductase
B: N-ethylmaleimide reductase
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,0566
Polymers118,6873
Non-polymers1,3693
Water59433
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0192
Polymers39,5621
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0192
Polymers39,5621
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0192
Polymers39,5621
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.488, 142.069, 87.871
Angle α, β, γ (deg.)90.000, 107.020, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 365 / Label seq-ID: 4 - 365

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC

-
Components

#1: Protein N-ethylmaleimide reductase / NEM reductase / N-ethylmaleimide reducing enzyme


Mass: 39562.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nemA, ydhN, b1650, JW1642 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P77258, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 175 mM malic acid, 18% PEG 3350

-
Data collection

DiffractionMean temperature: 77 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→19.9 Å / Num. obs: 27219 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 58.58 Å2 / Rpim(I) all: 0.109 / Rrim(I) all: 0.278 / Rsym value: 0.255 / Net I/av σ(I): 2.6 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.1-3.276.51.1110.72587439710.471.2091.1112100
3.27-3.476.10.77412281137620.340.8480.7742.799.5
3.47-3.716.60.5331.42314535150.2250.5790.5333.799.7
3.71-46.60.3372.12189633130.1420.3660.3375.499.8
4-4.386.60.2412.91987530290.1020.2620.2416.999.9
4.38-4.96.40.1733.61776027620.0740.1890.1738.699.7
4.9-5.666.50.1534.21573524140.0650.1670.1538.899.7
5.66-6.9370.144.41444020670.0570.1510.149.8100
6.93-9.86.40.1045.11032916040.0450.1140.10412.399.7
9.8-19.8966.40.0786.750397820.0330.0850.07816.388.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSBuilt=20200417data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P7Y

3p7y


Resolution: 3.1→19.9 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 1999 7.35 %
Rwork0.2297 25185 -
obs0.2321 27184 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.79 Å2 / Biso mean: 58.7287 Å2 / Biso min: 24.34 Å2
Refinement stepCycle: final / Resolution: 3.1→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8310 0 93 33 8436
Biso mean--46.15 50.67 -
Num. residues----1086
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5131X-RAY DIFFRACTION8.883TORSIONAL
12B5131X-RAY DIFFRACTION8.883TORSIONAL
13C5131X-RAY DIFFRACTION8.883TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.180.33911420.348517841926100
3.18-3.260.36591410.320517901931100
3.26-3.360.39481420.309517831925100
3.36-3.470.33331430.29171804194799
3.47-3.590.3221410.28281772191399
3.59-3.730.30121430.260517991942100
3.73-3.90.26411420.23771791193399
3.9-4.10.27931420.228318051947100
4.1-4.360.30871440.215418141958100
4.36-4.690.21461420.20217791921100
4.69-5.160.25561430.20621800194399
5.16-5.890.20381450.198118221967100
5.89-7.350.2321430.194518091952100
7.36-19.90.17111460.171118331979100

+
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