[English] 日本語
Yorodumi
- PDB-6k10: Non substrate bound state of Staphylococcus Aureus AldH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k10
TitleNon substrate bound state of Staphylococcus Aureus AldH
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / staphyloxanthin synthesis / dehydrogenase
Function / homology
Function and homology information


carotenoid biosynthetic process / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / aldehyde dehydrogenase (NAD+) activity / cytoplasm
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde dehydrogenase / 4,4'-diaponeurosporen-aldehyde dehydrogenase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78962181506 Å
AuthorsZhang, Z. / Tao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: CCS Chemistry / Year: 2020
Title: Structural Insight into the Substrate Gating Mechanism by Staphylococcus aureus Aldehyde Dehydrogenase
Authors: Tao, X. / Zhang, Z. / Zhang, X. / Li, H. / Sun, H. / Mao, Z. / Xia, W.
History
DepositionMay 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5642
Polymers52,5021
Non-polymers621
Water1,22568
1
A: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1284
Polymers105,0032
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_567x,-y+1,-z+21
Buried area8850 Å2
ΔGint-50 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.087, 95.245, 98.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein Aldehyde dehydrogenase /


Mass: 52501.684 Da / Num. of mol.: 1 / Mutation: C244S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HCL5, UniProt: Q2FWX9*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 40 % peg 400, 100 mM MES PH 5.5, 200 mM magnesium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 37718 / % possible obs: 98.9 % / Redundancy: 30.7 % / Biso Wilson estimate: 26.6330359311 Å2 / CC1/2: 0.962 / Net I/σ(I): 11
Reflection shellResolution: 1.79→1.85 Å / Num. unique obs: 3656 / CC1/2: 0.763

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78962181506→43.694173004 Å / SU ML: 0.184313269751 / Cross valid method: FREE R-VALUE / σ(F): 1.35401840812 / Phase error: 22.6035130451
RfactorNum. reflection% reflection
Rfree0.238888146277 1946 5.15934036799 %
Rwork0.213140790514 --
obs0.214450328416 37718 98.9039228026 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.7141634564 Å2
Refinement stepCycle: LAST / Resolution: 1.78962181506→43.694173004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 4 68 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002853114835543668
X-RAY DIFFRACTIONf_angle_d0.6631600118164981
X-RAY DIFFRACTIONf_chiral_restr0.0446198086619567
X-RAY DIFFRACTIONf_plane_restr0.0035836963606637
X-RAY DIFFRACTIONf_dihedral_angle_d17.30891348692187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7896-1.83440.3167850130011720.2760739625792414X-RAY DIFFRACTION96.4565460649
1.8344-1.8840.3017875987461460.2438998638442524X-RAY DIFFRACTION99.9251497006
1.884-1.93940.2382483483921180.2356790467072555X-RAY DIFFRACTION99.8878923767
1.9394-2.0020.267071699751180.2267492261332576X-RAY DIFFRACTION99.8517420311
2.002-2.07360.2242993717861540.2170100607792511X-RAY DIFFRACTION99.4032077583
2.0736-2.15660.233658963371360.20983539882516X-RAY DIFFRACTION99.4748687172
2.1566-2.25470.2375418300341650.206952063642543X-RAY DIFFRACTION99.889339727
2.2547-2.37360.2329640316531320.2190025517072576X-RAY DIFFRACTION99.889339727
2.3736-2.52230.2329079361841380.2091803251352556X-RAY DIFFRACTION99.7408367271
2.5223-2.7170.2392289928361230.2123266081072604X-RAY DIFFRACTION99.8169838946
2.717-2.99040.2182758631341260.2223899107162606X-RAY DIFFRACTION99.7444322746
2.9904-3.4230.2340375442291440.2152796034112593X-RAY DIFFRACTION99.4910941476
3.423-4.3120.2181882213791230.2053220021772544X-RAY DIFFRACTION95.831836148
4.312-43.70720.2521868200871510.2024754276292654X-RAY DIFFRACTION95.6358677122
Refinement TLS params.Method: refined / Origin x: 10.2021536231 Å / Origin y: 33.8886411323 Å / Origin z: 103.519878883 Å
111213212223313233
T0.132983877689 Å20.00967114674724 Å2-0.000586691194827 Å2-0.1403316925 Å2-0.00103838267565 Å2--0.127019147474 Å2
L0.154163905997 °20.0460560734837 °2-0.0452369524584 °2-0.297523770485 °2-0.0557781023115 °2--0.0229502341066 °2
S-0.0150029210042 Å °-0.00237882964706 Å °-0.0225318739107 Å °0.0369327179243 Å °0.0115246370442 Å °0.0205264586411 Å °-0.0139523167951 Å °0.00617129981431 Å °1.43437189258E-10 Å °
Refinement TLS groupSelection details: all

+
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