[English] 日本語
Yorodumi
- PDB-8i29: Crystal structure of butanol dehydrogenase A (YqdH) in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i29
TitleCrystal structure of butanol dehydrogenase A (YqdH) in complex with NADH from Fusobacterium nucleatum
ComponentsNADH-dependent butanol dehydrogenase A
KeywordsBIOSYNTHETIC PROTEIN / YqdH / NADH
Function / homology
Function and homology information


alcohol dehydrogenase [NAD(P)+] activity / methylglyoxal reductase (NADPH) (acetol producing) activity / butanol dehydrogenase (NAD+) activity / alcohol dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Butanol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / NADH-dependent butanol dehydrogenase A
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsBai, X. / Lan, J. / Bu, T.T. / Wang, L.L. / He, S.R. / Zhang, J. / Xu, Y.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of butanol dehydrogenase A (YqdH) in complex with NADH from Fusobacterium nucleatum
Authors: Bai, X. / Lan, J. / Bu, T.T. / He, S.R. / Zhang, J. / Wang, L.L.
History
DepositionJan 14, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 1, 2023ID: 7YIP
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADH-dependent butanol dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1895
Polymers43,3361
Non-polymers8534
Water1,18966
1
A: NADH-dependent butanol dehydrogenase A
hetero molecules

A: NADH-dependent butanol dehydrogenase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,37810
Polymers86,6722
Non-polymers1,7068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6390 Å2
ΔGint-89 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.426, 79.351, 212.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein NADH-dependent butanol dehydrogenase A


Mass: 43336.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Gene: FN1415 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q8R612, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 5 types, 70 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop / Details: ammonium phosphate, HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.719→35.53 Å / Num. obs: 14920 / % possible obs: 98.64 % / Redundancy: 12.4 % / CC1/2: 0.929 / CC star: 0.981 / Net I/σ(I): 11.88
Reflection shellResolution: 2.719→2.817 Å / Num. unique obs: 752 / CC1/2: 0.531

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L1K

6l1k


Resolution: 2.72→35.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.462 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.016 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25799 1493 10 %RANDOM
Rwork0.19738 ---
obs0.20356 13427 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.195 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0 Å2
2---0.33 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.72→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 51 66 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123116
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162971
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.6364215
X-RAY DIFFRACTIONr_angle_other_deg0.4911.5686857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.074510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01510555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
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_it4.9945.6461535
X-RAY DIFFRACTIONr_mcbond_other4.9915.6461535
X-RAY DIFFRACTIONr_mcangle_it7.44810.1461917
X-RAY DIFFRACTIONr_mcangle_other7.44710.1451918
X-RAY DIFFRACTIONr_scbond_it5.9746.111581
X-RAY DIFFRACTIONr_scbond_other5.9356.1081578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.85811.0972293
X-RAY DIFFRACTIONr_long_range_B_refined11.67453.693618
X-RAY DIFFRACTIONr_long_range_B_other11.63353.343610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.79 Å
RfactorNum. reflection% reflection
Rfree0.319 91 -
Rwork0.292 813 -
obs--83.16 %

+
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://pdbjlvh1.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