[English] 日本語
Yorodumi
- PDB-1bg6: CRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bg6
TitleCRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE FROM ARTHROBACTER SP. STRAIN 1C
ComponentsN-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / (D / L) STEREOSPECIFIC OPINE DEHYDROGENASE
Function / homology
Function and homology information


opine dehydrogenase / opine dehydrogenase activity
Similarity search - Function
Opine dehydrogenase / : / NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Opine dehydrogenase / : / NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsBritton, K.L. / Asano, Y. / Rice, D.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure and active site location of N-(1-D-carboxylethyl)-L-norvaline dehydrogenase.
Authors: Britton, K.L. / Asano, Y. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization of Arthrobacter Sp. Strain 1C N-(1-D-Carboxyethyl)-L-Norvaline Dehydrogenase and its Complex with Nad+
Authors: Britton, K.L. / Rogers, H.F. / Asano, Y. / Dairi, T. / Kato, Y. / Stillman, T.J. / Rice, D.W.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)37,9691
Polymers37,9691
Non-polymers00
Water2,036113
1
A: N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE

A: N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)75,9382
Polymers75,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)104.900, 80.000, 45.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE


Mass: 37969.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: 1C / Gene: ODH / Plasmid: PODH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q44297
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 41 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Mpotassium phosphate1drop
336-37 %satammonium sulfate1reservoir
40.1 Mpotassium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→16 Å / Num. obs: 30854 / % possible obs: 89 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5 / % possible all: 78
Reflection
*PLUS
Num. measured all: 66518
Reflection shell
*PLUS
% possible obs: 78 %

-
Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
Num. reflection% reflection
all31467 -
obs28922 83 %
Solvent computationBsol: 310 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 0 113 2705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg1.65
X-RAY DIFFRACTIONt_dihedral_angle_d17.47
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2545 / % reflection Rfree: 8 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.47
X-RAY DIFFRACTIONt_plane_restr0.016

+
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