[English] 日本語
Yorodumi
- PDB-4nfs: V203A horse liver alcohol dehydrogenase E complexed with NAD and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nfs
TitleV203A horse liver alcohol dehydrogenase E complexed with NAD and 2,2,2-trifluoroethanol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Rossmann fold / dehydrogenase / NAD / liver cytosol
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
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
TRIFLUOROETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsPlapp, B.V.
CitationJournal: Biochemistry / Year: 2014
Title: Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis.
Authors: Yahashiri, A. / Rubach, J.K. / Plapp, B.V.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.pdbx_ptnr1_label_alt_id / _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.ptnr1_label_seq_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_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: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,91214
Polymers79,6502
Non-polymers2,26112
Water18,6281034
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-112 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.280, 51.410, 92.530
Angle α, β, γ (deg.)91.88, 103.09, 109.94
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 39825.223 Da / Num. of mol.: 2 / Mutation: V203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Strain: domestic horse / Plasmid: pBBP/EqADH E / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

-
Non-polymers , 5 types, 1046 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#4: Chemical ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 50 mN ammonium N-[tris(hydroxymethyl)methyl]-2-amminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 13-25 % 2-methyl-2,4- ...Details: 50 mN ammonium N-[tris(hydroxymethyl)methyl]-2-amminoethanesulfonate and 0.5 mM EDTA, pH 6.7 (at 25 deg C), 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 13-25 % 2-methyl-2,4-methylpentanediol, MICRODIALYSIS, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.802 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 13, 2007 / Details: Rosenbaum-Rock vertically focussed mirrors
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focussed / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. all: 310308 / Num. obs: 266123 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.05 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.2
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.2 / Num. unique all: 15266 / % possible all: 50.6

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.7.0032refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DXH

4dxh


Resolution: 1.1→19.58 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.052 / SU ML: 0.022 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17474 2690 1 %RANDOM
Rwork0.13743 ---
obs0.13781 263388 88.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0.08 Å2-0.02 Å2
2--0.21 Å2-0.34 Å2
3----0.16 Å2
Refine analyzeLuzzati coordinate error free: 0.033 Å
Refinement stepCycle: LAST / Resolution: 1.1→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 136 1034 6736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.026079
X-RAY DIFFRACTIONr_bond_other_d0.0020.026025
X-RAY DIFFRACTIONr_angle_refined_deg1.9332.0168255
X-RAY DIFFRACTIONr_angle_other_deg0.927314018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07124.558215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.105151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3551527
X-RAY DIFFRACTIONr_chiral_restr0.1210.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021209
X-RAY DIFFRACTIONr_mcbond_it1.6571.3893041
X-RAY DIFFRACTIONr_mcbond_other1.6571.3893040
X-RAY DIFFRACTIONr_mcangle_it1.7552.0943811
X-RAY DIFFRACTIONr_mcangle_other1.7552.0943812
X-RAY DIFFRACTIONr_scbond_it3.171.7393038
X-RAY DIFFRACTIONr_scbond_other3.1711.743039
X-RAY DIFFRACTIONr_scangle_other3.3382.484439
X-RAY DIFFRACTIONr_long_range_B_refined5.86814.4197917
X-RAY DIFFRACTIONr_long_range_B_other4.21812.617156
X-RAY DIFFRACTIONr_rigid_bond_restr12.098312104
X-RAY DIFFRACTIONr_sphericity_free53.32210236
X-RAY DIFFRACTIONr_sphericity_bonded13.9321012813
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 109 -
Rwork0.345 10674 -
obs--48.44 %

+
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