[English] 日本語
Yorodumi
- PDB-5cds: I220L horse liver alcohol dehydrogenase complexed with NAD and pe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cds
TitleI220L horse liver alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol / Rossmann fold
Function / homology
Function and homology information


alcohol dehydrogenase activity, zinc-dependent / ethanol oxidation / NAD-retinol dehydrogenase 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPlapp, B.V. / Shanmuganatham, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 078446 United States
CitationJournal: Protein Sci. / Year: 2017
Title: Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis.
Authors: Shanmuganatham, K.K. / Wallace, R.S. / Lee, A.T. / Plapp, B.V.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
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)81,92812
Polymers79,7072
Non-polymers2,22110
Water15,565864
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-19 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.270, 51.530, 92.440
Angle α, β, γ (deg.)91.75, 103.12, 109.34
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 2 / Mutation: I220L
Source method: isolated from a genetically manipulated source
Details: I220F substitution of wild-type horse liver alcohol dehydrogenase E1
Source: (gene. exp.) Equus caballus (horse) / Organ: Liver / Plasmid: pBPP/EqADH1E / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

-
Non-polymers , 5 types, 874 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-PFB / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL


Mass: 198.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H3F5O
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: columns
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-,4-PENTANEDIOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.8 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 132451 / % possible obs: 91 % / Redundancy: 3.64 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.3
Reflection shellResolution: 1.4→1.436 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.3 / % possible all: 86.77

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
d*TREKdata reduction
d*TREKdata scaling
Omodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV
Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.816 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18411 1340 1 %RANDOM
Rwork0.13194 ---
obs0.13246 132451 91.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.63 Å2-0.14 Å2
2--1.57 Å2-0.08 Å2
3----2.09 Å2
Refinement stepCycle: 1 / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 134 864 6568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025934
X-RAY DIFFRACTIONr_bond_other_d0.0010.025847
X-RAY DIFFRACTIONr_angle_refined_deg1.7022.0178046
X-RAY DIFFRACTIONr_angle_other_deg0.877313578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86724.581203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.072151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4741524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021176
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1272.0072994
X-RAY DIFFRACTIONr_mcbond_other2.1272.0062993
X-RAY DIFFRACTIONr_mcangle_it2.3563.0233740
X-RAY DIFFRACTIONr_mcangle_other2.3563.0233741
X-RAY DIFFRACTIONr_scbond_it3.5752.3542940
X-RAY DIFFRACTIONr_scbond_other3.5812.3552941
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8993.3934305
X-RAY DIFFRACTIONr_long_range_B_refined4.37818.7337488
X-RAY DIFFRACTIONr_long_range_B_other3.78917.3676901
X-RAY DIFFRACTIONr_rigid_bond_restr3.726311781
X-RAY DIFFRACTIONr_sphericity_free30.41210203
X-RAY DIFFRACTIONr_sphericity_bonded10.3021012361
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 99 -
Rwork0.271 9313 -
obs--86.77 %

+
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