[English] 日本語
Yorodumi
- PDB-7tmb: Crystal Structure of N-ethylmaleimide reductase from Klebsiella p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tmb
TitleCrystal Structure of N-ethylmaleimide reductase from Klebsiella pneumoniae
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / N-ethylmaleimide reductase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / 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
CITRATE ANION / FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal Structure of N-ethylmaleimide reductase from Klebsiella pneumoniae
Authors: Lovell, S. / Liu, L. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)249,21136
Polymers242,8706
Non-polymers6,34130
Water25,4911415
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3465
Polymers40,4781
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7247
Polymers40,4781
Non-polymers1,2466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5356
Polymers40,4781
Non-polymers1,0575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.307, 223.870, 223.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
N-ethylmaleimide reductase


Mass: 40478.305 Da / Num. of mol.: 6 / Fragment: KlpnC.00093.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_29700 / Plasmid: KlpnC.00093.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GQS4

-
Non-polymers , 5 types, 1445 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1415 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.6 % / Mosaicity: 0.11 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Index H10: 20 % (w/v) PEG 3350, 0.2 M Sodium citrate tribasic dihydrate, KlpnC.00093.a.B1.PS39081 at 18.3 mg/mL, Tray: plate 12226 well H10 drop 1, Puck: PSL0405, Cryo: 80% crystallant and 20% PEG 200,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→49.24 Å / Num. obs: 190392 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10 / Num. measured all: 1290315 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.1-2.146.60.846144093410.8722.199.9
11.5-49.246.30.035806112710.99927.198.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.20_4474refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P62

3p62


Resolution: 2.1→25.54 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 9429 4.97 %
Rwork0.1923 180468 -
obs0.1943 189897 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.83 Å2 / Biso mean: 30.6636 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 2.1→25.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16390 0 395 1415 18200
Biso mean--49.48 32.77 -
Num. residues----2165
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 (%)
2.1-2.120.30593350.270559376272100
2.12-2.150.27272690.254160036272100
2.15-2.180.28573000.253659996299100
2.18-2.20.28413190.243959516270100
2.2-2.230.27773220.242759836305100
2.23-2.260.29283230.229959426265100
2.26-2.290.26942750.223260106285100
2.29-2.330.27412760.216860466322100
2.33-2.360.2443120.212159786290100
2.36-2.40.24633520.218359596311100
2.4-2.450.26373190.216859856304100
2.45-2.490.25963230.210359596282100
2.49-2.540.2773190.206159996318100
2.54-2.590.27863010.21459776278100
2.59-2.650.27672980.211660106308100
2.65-2.710.26533380.201759846322100
2.71-2.770.22662480.20360506298100
2.77-2.850.2412640.202460526316100
2.85-2.930.23753180.193460066324100
2.93-3.030.23033190.202460456364100
3.03-3.140.24943420.203459706312100
3.14-3.260.23262910.206960336324100
3.26-3.410.23863560.199460236379100
3.41-3.590.21713080.187660446352100
3.59-3.810.22293600.17160016361100
3.81-4.110.1763180.152160656383100
4.11-4.520.1863050.141660966401100
4.52-5.170.17253590.144760616420100
5.17-6.490.20463110.165361766487100
6.49-25.540.20533490.18596124647397

+
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