[English] 日本語
Yorodumi
- PDB-9ix7: Crystal structure of homolog of dihydroxyacid dehydratase(AstD) f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ix7
TitleCrystal structure of homolog of dihydroxyacid dehydratase(AstD) from Aspergillus terreus
Componentsdihydroxy-acid dehydratase
KeywordsLYASE / dihydroxyacid dehydratase
Function / homology
Function and homology information


dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / L-valine biosynthetic process / isoleucine biosynthetic process / 2 iron, 2 sulfur cluster binding / mitochondrion / metal ion binding
Similarity search - Function
Dihydroxy-acid dehydratase / : / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2. / Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. / : / Dihydroxy-acid/6-phosphogluconate dehydratase C-terminal / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dihydroxy-acid/6-phosphogluconate dehydratase N-terminal
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / dihydroxy-acid dehydratase
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHuang, W.X. / Zhang, P.X. / Zhou, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071446 China
CitationJournal: Biodes Res / Year: 2024
Title: Structural Bases of Dihydroxy Acid Dehydratase Inhibition and Biodesign for Self-Resistance.
Authors: Zang, X. / Bat-Erdene, U. / Huang, W. / Wu, Z. / Jacobsen, S.E. / Tang, Y. / Zhou, J.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dihydroxy-acid dehydratase
B: dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6846
Polymers120,3922
Non-polymers2924
Water6,251347
1
A: dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3643
Polymers60,1961
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dihydroxy-acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3203
Polymers60,1961
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-16 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.614, 66.278, 268.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLU(chain 'A' and (resid 69 through 79 or (resid 80...AA69 - 8231 - 44
12HISHISSERSER(chain 'A' and (resid 69 through 79 or (resid 80...AA91 - 11753 - 79
13LYSLYSILEILE(chain 'A' and (resid 69 through 79 or (resid 80...AA125 - 18587 - 147
14ALAALAARGARG(chain 'A' and (resid 69 through 79 or (resid 80...AA238 - 292200 - 254
15ALAALAILEILE(chain 'A' and (resid 69 through 79 or (resid 80...AA294 - 598256 - 560
16EDOEDOEDOEDO(chain 'A' and (resid 69 through 79 or (resid 80...AD602
27METMETGLUGLU(chain 'B' and (resid 69 through 160 or (resid 161...BB69 - 8231 - 44
28HISHISSERSER(chain 'B' and (resid 69 through 160 or (resid 161...BB91 - 11753 - 79
29LYSLYSILEILE(chain 'B' and (resid 69 through 160 or (resid 161...BB125 - 18587 - 147
210ALAALAARGARG(chain 'B' and (resid 69 through 160 or (resid 161...BB238 - 292200 - 254
211ALAALAILEILE(chain 'B' and (resid 69 through 160 or (resid 161...BB294 - 598256 - 560
212EDOEDOEDOEDO(chain 'B' and (resid 69 through 160 or (resid 161...BF602

-
Components

#1: Protein dihydroxy-acid dehydratase


Mass: 60195.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: ATEIFO6365_0004000400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5M3YPM6, dihydroxy-acid dehydratase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: MMT pH4.0 ,17% PEG1500, 1mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→47.2 Å / Num. obs: 45340 / % possible obs: 96.97 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.81 Å2 / Rmerge(I) obs: 0.185 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.04 / Num. unique obs: 3599

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
PHASESphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YMO

5ymo
PDB Unreleased entry


Resolution: 2.29→47.2 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6065
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 2294 5.06 %
Rwork0.2008 43029 -
obs0.2023 45323 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.92 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6945 0 19 347 7311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247086
X-RAY DIFFRACTIONf_angle_d0.64179572
X-RAY DIFFRACTIONf_chiral_restr0.04571090
X-RAY DIFFRACTIONf_plane_restr0.0041247
X-RAY DIFFRACTIONf_dihedral_angle_d17.67024327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.340.31251060.2631960X-RAY DIFFRACTION72.47
2.34-2.390.26491420.25322389X-RAY DIFFRACTION89.03
2.39-2.450.28641200.25722639X-RAY DIFFRACTION95.34
2.45-2.520.29111580.24582658X-RAY DIFFRACTION98.26
2.52-2.590.24651440.24282730X-RAY DIFFRACTION99.48
2.59-2.680.28331290.24432750X-RAY DIFFRACTION99.79
2.68-2.770.26481470.24362729X-RAY DIFFRACTION99.86
2.77-2.880.29251410.2342768X-RAY DIFFRACTION99.86
2.88-3.020.2931600.22932732X-RAY DIFFRACTION99.93
3.02-3.170.23821480.2142748X-RAY DIFFRACTION99.93
3.17-3.370.20761560.20762758X-RAY DIFFRACTION99.9
3.37-3.630.22271430.19252780X-RAY DIFFRACTION99.86
3.63-40.22261550.17132779X-RAY DIFFRACTION99.86
4-4.580.20921450.16152803X-RAY DIFFRACTION99.59
4.58-5.770.18091460.16962846X-RAY DIFFRACTION99.37
5.77-47.20.19081540.17922960X-RAY DIFFRACTION98.48
Refinement TLS params.Method: refined / Origin x: 0.0595562265417 Å / Origin y: 6.54804493785 Å / Origin z: 31.1419449094 Å
111213212223313233
T0.222520945577 Å2-0.00256759500025 Å2-0.0172976587248 Å2-0.248502046999 Å2-0.0136053827726 Å2--0.228391428836 Å2
L0.367849604575 °2-0.0604462383379 °2-0.021940454197 °2-0.700424665132 °20.161548638389 °2--0.354390394662 °2
S-0.0204219121202 Å °-0.00539430134682 Å °-0.0520605925625 Å °0.071757091828 Å °0.0128060889427 Å °-0.0496334137097 Å °0.0404222911583 Å °-0.0470329445581 Å °0.00725955329206 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