[English] 日本語
Yorodumi
- PDB-6owm: Horse liver F93W alcohol dehydrogenase complexed with NAD and pen... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6owm
TitleHorse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / NAD / pentafluorobenzyl alcohol / Phe93 to Trp substitution / Horse liver E enzyme
Function / homology
Function and homology information


retinoic acid metabolic process / alcohol dehydrogenase activity, zinc-dependent / ethanol oxidation / alcohol dehydrogenase / retinol dehydrogenase activity / retinol metabolic process / zinc ion binding / cytosol
GroES-like superfamily / Polyketide synthase, enoylreductase domain / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase GroES-like domain / Zinc-binding dehydrogenase / NAD(P)-binding domain superfamily / Alcohol dehydrogenase, zinc-type, conserved site / Alcohol dehydrogenase, C-terminal / Alcohol dehydrogenase, N-terminal
Alcohol dehydrogenase E chain
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsPlapp, B.V.
Funding supportUnited States , 2件
OrganizationGrant numberCountry
Department of Health & Human ServicesAA00279United States
Department of Health & Human ServicesGM078446United States
Citation
Journal: To Be Published
Title: Substitutions of amino acid residues in the substrate binding site of horse liver alcohol dehydrogenase have small effects on structure but significantly affect catalysis of hydrogen transfer.
Authors: Plapp, B.V. / Kim, K.
#1: Journal: Biochemistry / Year: 1993
Title: Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis.
Authors: Bahnson, B.J. / Park, D.H. / Kim, K. / Plapp, B.V. / Klinman, J.P.
#2: Journal: Biochemistry / Year: 2012
Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.
Authors: Plapp, B.V. / Ramaswamy, S.
#3: Journal: Isotope Effects in Chemistry and Biology / Year: 2006
Title: Catalysis by Alcohol Dehydrogenases
Authors: Plapp, B.V.
#4: Journal: Chem. Biol. Interact. / Year: 2017
Title: Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93.
Authors: Kim, K. / Plapp, B.V.
#5: Journal: Biochemistry / Year: 1998
Title: Active site modifications in a double mutant of liver alcohol dehydrogenase: structural studies of two enzyme-ligand complexes.
Authors: Colby, T.D. / Bahnson, B.J. / Chin, J.K. / Klinman, J.P. / Goldstein, B.M.
#6: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1997
Title: A link between protein structure and enzyme catalyzed hydrogen tunneling.
Authors: Bahnson, B.J. / Colby, T.D. / Chin, J.K. / Goldstein, B.M. / Klinman, J.P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 10, 2019 / Release: May 22, 2019
RevisionDateData content typeProviderType
1.0May 22, 2019Structure modelrepositoryInitial release

-
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)82,12413
Polymers79,7852
Non-polymers2,33911
Water18,4471024
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-112 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)44.470, 51.440, 92.560
Angle α, β, γ (deg.)92.09, 102.95, 110.25
Int Tables number1
Space group name H-MP1

-
Components

-
Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide Alcohol dehydrogenase E chain


Mass: 39892.309 Da / Num. of mol.: 2 / Mutation: F93W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / Variant (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

-
Non-polymers , 5 types, 1035 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / 2-Methyl-2,4-pentanediol
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1024 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.91 % / Description: block
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7
Details: 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethane sulfonate, 0.25 mM EDTA, pH 6.7 at 25 deg C, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 14 to 25 % 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: adjustable foculs K-B pari SiPlus PT, RH coatings
RadiationMonochromator: double crystal cryocooled Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.1→19.62 Å / Num. obs: 267734 / % possible obs: 88.6 % / Redundancy: 5.15 % / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.082 / Χ2: 1.15 / Net I/σ(I): 11.4 / Num. measured all: 1394329 / Scaling rejects: 16553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.1-1.143.440.283.159197171940.3291.444456.8
1.14-1.183.530.2023.993072263430.2371.242787.4
1.18-1.243.830.1674.8103993271690.1941.191889.8
1.24-1.33.840.1445.6105191273970.1671.145990.7
1.3-1.393.850.1216.7107187277970.141.0917191.7
1.39-1.493.870.1057.4108886280340.1220.9328392.8
1.49-1.646.730.1548.9191695283530.1671.2389993.9
1.64-1.887.740.09713.8225658287830.1041.11292195.4
1.88-2.377.570.07219.4227174292150.0771.12605396.6
2.37-19.626.050.06221172276274490.0691.2607890.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
d*TREK9.9.9.8Ldata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
Omodel building
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6o91
Resolution: 1.1→19.62 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.742 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14059 2622 1 %RANDOM
Rwork0.12386 ---
Obs0.12402 265082 88.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0.54 Å20.31 Å2
2--0.46 Å20.12 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.1→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 142 1024 6742
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0130.0136273
r_bond_other_d0.0010.0176067
r_angle_refined_deg1.8431.6888549
r_angle_other_deg1.5411.59114211
r_dihedral_angle_1_deg17.8445.377836
r_dihedral_angle_2_deg35.79423.178236
r_dihedral_angle_3_deg10.888151124
r_dihedral_angle_4_deg13.5311525
r_chiral_restr0.1070.2865
r_gen_planes_refined0.0090.027608
r_gen_planes_other0.0020.021149
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.9871.3743143
r_mcbond_other0.9851.3733142
r_mcangle_it1.2042.0713944
r_mcangle_other1.2042.0713945
r_scbond_it1.6761.6463130
r_scbond_other1.6751.6473131
r_scangle_it
r_scangle_other1.9452.3714585
r_long_range_B_refined2.58918.7417225
r_long_range_B_other2.16517.3786884
r_rigid_bond_restr2.481312338
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 123 -
Rwork0.285 11720 -
Obs--53.11 %

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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