[English] 日本語
Yorodumi
- PDB-6fg0: Crystal structure of R. ruber ADH-A, mutant Y54G, F43T, L119Y, F282W -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fg0
TitleCrystal structure of R. ruber ADH-A, mutant Y54G, F43T, L119Y, F282W
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase mutant variant / NADH-dependent / Zn2+-dependent / Rossmann fold
Function / homology
Function and homology information


oxidoreductase activity / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase
Similarity search - Component
Biological speciesRhodococcus sp. M8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsDobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / Widersten, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Acs Catalysis / Year: 2018
Title: Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases
Authors: Maurer, D. / Enugala, T.R. / Hamnevik, E. / Bauer, P. / Luking, M. / Hillier, H. / Kamerlin, S.C.L. / Dobritzsch, D. / Widersten, M.
History
DepositionJan 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
C: Alcohol dehydrogenase
D: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,32516
Polymers144,1484
Non-polymers3,17712
Water24,8791381
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint-260 kcal/mol
Surface area44800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.706, 105.463, 108.977
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1 - 3461 - 346
21THRTHRBB1 - 3461 - 346
12THRTHRAA1 - 3461 - 346
22THRTHRCC1 - 3461 - 346
13VALVALAA1 - 3441 - 344
23VALVALDD1 - 3441 - 344
14THRTHRBB1 - 3461 - 346
24THRTHRCC1 - 3461 - 346
15VALVALBB1 - 3441 - 344
25VALVALDD1 - 3441 - 344
16VALVALCC1 - 3441 - 344
26VALVALDD1 - 3441 - 344

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Alcohol dehydrogenase /


Mass: 36036.887 Da / Num. of mol.: 4 / Mutation: Y54G, L119Y, F43T, F282W
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag / Source: (gene. exp.) Rhodococcus sp. M8 (bacteria) / Gene: BKE56_025765 / Plasmid: pGT7ADHA-5H / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: A0A1Q8I6M1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1381 / 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: 2.35 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 15% Polyacrylic acid 510 100 mM Tris pH 8 4 mM NAD+ 10 mM MgCl2 3 mg/ml ADHA mutant

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.74→29.5 Å / Num. obs: 143025 / % possible obs: 94.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.036 / Rrim(I) all: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4568 / CC1/2: 0.603 / Rpim(I) all: 0.435 / Rrim(I) all: 0.736 / % possible all: 60.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3jv7

3jv7


Resolution: 1.74→29.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.501 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18132 7493 5.2 %RANDOM
Rwork0.16289 ---
obs0.16388 135478 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.156 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0 Å20.34 Å2
2--1.12 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.74→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9893 0 184 1381 11458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910318
X-RAY DIFFRACTIONr_bond_other_d0.0020.029670
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.98514131
X-RAY DIFFRACTIONr_angle_other_deg0.945322266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84451385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77722.765358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.655151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3521573
X-RAY DIFFRACTIONr_chiral_restr0.0770.21654
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022065
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_it0.6711.535540
X-RAY DIFFRACTIONr_mcbond_other0.671.5295539
X-RAY DIFFRACTIONr_mcangle_it1.1282.296922
X-RAY DIFFRACTIONr_mcangle_other1.1282.2916923
X-RAY DIFFRACTIONr_scbond_it0.861.6314778
X-RAY DIFFRACTIONr_scbond_other0.861.6314779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.412.4067209
X-RAY DIFFRACTIONr_long_range_B_refined5.33820.63211598
X-RAY DIFFRACTIONr_long_range_B_other5.03119.09911107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A208800.04
12B208800.04
21A208760.04
22C208760.04
31A206840.04
32D206840.04
41B207460.05
42C207460.05
51B207360.03
52D207360.03
61C205380.05
62D205380.05
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 386 -
Rwork0.285 6713 -
obs--63.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8511-0.1835-0.13990.79780.18451.2889-0.030.0242-0.1888-0.0517-0.0154-0.02220.16620.03440.04540.11440.00030.01870.0041-0.00270.0487-4.684919.0943-31.0258
20.83840.24330.05960.85690.12061.28520.0155-0.01820.13560.07-0.0118-0.0389-0.15930.0606-0.00380.1116-0.0232-0.01420.0075-0.00010.0313-1.957860.2246-23.6891
31.3791-0.16440.08551.16780.14430.72110.04450.38210.0047-0.2199-0.05630.1360.0001-0.11250.01190.1344-0.0026-0.0340.16590.01910.0257-30.19745.6708-49.3201
41.60910.30970.10141.292-0.13920.85340.0257-0.40330.05050.2853-0.01110.2125-0.0927-0.2105-0.01450.15290.01070.03490.17070.01870.0525-32.931337.9832-8.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 503
2X-RAY DIFFRACTION2B1 - 503
3X-RAY DIFFRACTION3C1 - 503
4X-RAY DIFFRACTION4D1 - 503

+
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