[English] 日本語
Yorodumi
- PDB-3gka: Crystal structure of N-ethylmaleimidine reductase from Burkholder... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gka
TitleCrystal structure of N-ethylmaleimidine reductase from Burkholderia pseudomallei
ComponentsN-ethylmaleimide reductase
KeywordsOXIDOREDUCTASE / deCODE biostructures / SSGCID / NIAID / targetDB BupsA00093a / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases / 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / N-ethylmaleimide reductase / N-ethylmaleimide reductase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of N-ethylmaleimidine reductase from Burkholderia pseudomallei
Authors: Edwards, T.E. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: N-ethylmaleimide reductase
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1274
Polymers77,2152
Non-polymers9132
Water7,152397
1
A: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0642
Polymers38,6071
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-ethylmaleimide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0642
Polymers38,6071
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.350, 77.890, 168.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein N-ethylmaleimide reductase


Mass: 38607.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BPSS0877 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63LY5, UniProt: Q3JFM9*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ sparse matrix screen condition H3, 25% PEG3350, 0.1M BisTris pH 5.5, 12.2 mg/mL BupsA00093aB1, crystal ID 200758h3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29741 / % possible obs: 99.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.82
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.97 / Num. unique all: 2179 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.7 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.55 Å
Translation3 Å19.55 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R14

2r14


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / SU B: 6.147 / SU ML: 0.153 / SU R Cruickshank DPI: 0.433 / SU Rfree: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1506 5.1 %RANDOM
Rwork0.176 ---
obs0.18 29688 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.98 Å2 / Biso mean: 14.258 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--0.93 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 62 397 5735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225474
X-RAY DIFFRACTIONr_bond_other_d0.0010.023630
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.9637485
X-RAY DIFFRACTIONr_angle_other_deg0.85338749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6915703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89522.61249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4671554
X-RAY DIFFRACTIONr_chiral_restr0.0620.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021187
X-RAY DIFFRACTIONr_mcbond_it0.3821.53491
X-RAY DIFFRACTIONr_mcbond_other0.0631.51428
X-RAY DIFFRACTIONr_mcangle_it0.7425545
X-RAY DIFFRACTIONr_scbond_it1.20731983
X-RAY DIFFRACTIONr_scangle_it2.074.51940
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 104 -
Rwork0.209 2071 -
all-2175 -
obs--99.68 %

+
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