[English] 日本語
Yorodumi
- PDB-3f7j: B.subtilis YvgN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f7j
TitleB.subtilis YvgN
ComponentsYvgN protein
KeywordsOXIDOREDUCTASE / Aldo-keto Reductase
Function / homology
Function and homology information


methylglyoxal reductase (NADPH) / methylglyoxal reductase (NADPH) activity / small molecule metabolic process / : / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
Aldo-keto reductase family 5G / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 5G / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / NITRATE ION / Glyoxal reductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsZhou, Y.F. / Lei, J. / Liang, Y.H. / Su, X.-D.
CitationJournal: Protein Sci. / Year: 2009
Title: Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis
Authors: Lei, J. / Zhou, Y.F. / Li, L.F. / Su, X.-D.
History
DepositionNov 9, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionNov 25, 2008ID: 3B3E
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: YvgN protein
B: YvgN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,04813
Polymers63,4122
Non-polymers63611
Water9,512528
1
A: YvgN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0166
Polymers31,7061
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YvgN protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0327
Polymers31,7061
Non-polymers3266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.656, 123.075, 57.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-281-

NO3

21A-281-

NO3

31A-661-

HOH

-
Components

#1: Protein YvgN protein / Putative reductase protein / YvgN


Mass: 31705.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yvgN / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32210
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris, 0.4M sodium nitrate, 40% PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.96 Å
DetectorType: Mar / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.7→66.872 Å / Num. obs: 60078 / % possible obs: 96.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 9.308
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.795.20.4931.64443785200.49394.5
1.79-1.95.30.3092.54237080500.30994.4
1.9-2.035.30.2073.44046276760.20795.5
2.03-2.195.30.1365.53840072630.13697
2.19-2.45.30.1017.23614367920.10198
2.4-2.695.40.0779.53320161600.07798.3
2.69-3.15.50.05213.22965054360.05297.6
3.1-3.85.50.036162517946100.03696.8
3.8-5.385.50.02720.91943735600.02795.7
5.38-37.095.30.02917.11063720110.02993.6

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
MOLREPphasing
RefinementResolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.252 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1813 3 %RANDOM
Rwork0.212 ---
obs0.214 59998 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 29.12 Å2 / Biso mean: 4.548 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---0.58 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4468 0 38 528 5034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224600
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9636208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09125.526228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93415857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3671520
X-RAY DIFFRACTIONr_chiral_restr0.1970.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023486
X-RAY DIFFRACTIONr_nbd_refined0.280.22756
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2510.2512
X-RAY DIFFRACTIONr_metal_ion_refined0.3290.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.224
X-RAY DIFFRACTIONr_mcbond_it0.5961.52781
X-RAY DIFFRACTIONr_mcangle_it1.03724447
X-RAY DIFFRACTIONr_scbond_it1.98631835
X-RAY DIFFRACTIONr_scangle_it3.0944.51759
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 103 -
Rwork0.31 4191 -
all-4294 -
obs--94.15 %
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)
10.62010.2249-0.1642.45860.87062.8088-0.0337-0.00990.0245-0.2088-0.02260.07130.155-0.07930.0563-0.19510.0146-0.006-0.14630.0053-0.1248-17.648310.2456-22.1653
20.5748-0.31530.12362.24991.0962.91420.0214-0.00570.0082-0.148-0.04460.0456-0.1837-0.05030.0232-0.17-0.00220.0032-0.14990.005-0.1154-18.42241.247-6.4538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B1 - 276

+
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