[English] 日本語
Yorodumi
- PDB-1nvg: N249Y MUTANT OF THE ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nvg
TitleN249Y MUTANT OF THE ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS-TETRAGONAL CRYSTAL FORM
ComponentsNAD-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / ARCHAEON / ZINC / NAD(H) dependent / mutant
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD-dependent alcohol dehydrogenase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEsposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
Citation
Journal: Febs Lett. / Year: 2003
Title: Structural study of a single-point mutant of Sulfolobus solfataricus alcohol dehydrogenase with enhanced activity
Authors: Esposito, L. / Bruno, I. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure of Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Sulfolobus Solfataricus at 1.85 Angstrom Resolution
Authors: Esposito, L. / Sica, F. / Raia, C.A. / Giordano, A. / Rossi, M. / Mazzarella, L. / Zagari, A.
#2: Journal: Biochemistry / Year: 1999
Title: Asn249Tyr Substitution at the Coenzyme Binding Domain Activates Sulfolobus Solfataricus Alcohol Dehydrogenase and Increases its Thermal Stability
Authors: Giordano, A. / Cannio, R. / La Cara, F. / Bartolucci, S. / Rossi, M. / Raia, C.A.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Three Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstrom Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
History
DepositionFeb 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 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: NAD-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7953
Polymers37,6651
Non-polymers1312
Water2,162120
1
A: NAD-dependent alcohol dehydrogenase
hetero molecules

A: NAD-dependent alcohol dehydrogenase
hetero molecules

A: NAD-dependent alcohol dehydrogenase
hetero molecules

A: NAD-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,18212
Polymers150,6584
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation15_555y,x,-z1
crystal symmetry operation10_555-x,-y,z1
Unit cell
Length a, b, c (Å)125.396, 125.396, 117.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a tetramer generated from chain A in the asymmetric unit by the following symmetry operations: -y,-x,-z; y,x,-z; -x,-y, z.

-
Components

#1: Protein NAD-dependent alcohol dehydrogenase


Mass: 37664.594 Da / Num. of mol.: 1 / Mutation: N249Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: ADH OR SSO2536 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): RB791 / References: UniProt: P39462, alcohol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 296 K / Method: batch
Details: 7% (W/V) PEG 4000, 7% (V/V) ISOPROPANOL, 50mM SODIUM CITRATE PH 5.6, 50mM TRIS PH 7.8, pH NULL, BATCH, temperature 296K
Crystal grow
*PLUS
Details: Pearl, L., (1993) J. Mol. Biol., 229, 782.

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 15757 / Num. obs: 15757 / % possible obs: 95 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 32.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 16.3 / Num. unique all: 1584 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. measured all: 104158
Reflection shell
*PLUS
% possible obs: 96.9 % / Mean I/σ(I) obs: 16

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTO

1nto


Resolution: 2.5→25 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1230 7.9 %RANDOM
Rwork0.196 ---
all0.203 ---
obs0.196 15490 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å20 Å20 Å2
2--2.86 Å20 Å2
3----5.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 2 120 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.962.5
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.346 121 7.9 %
Rwork0.26 1411 -
obs-1532 94.6 %
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

+
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