[English] 日本語
Yorodumi
- PDB-8swm: Crystal structure of Campylobacter jejuni ketol-acid reductoisome... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8swm
TitleCrystal structure of Campylobacter jejuni ketol-acid reductoisomerase in complex with 2-acetolactate
ComponentsKetol-acid reductoisomerase (NADP(+))
KeywordsOXIDOREDUCTASE / Inhibitor / Biofuel / Enzyme
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / L-valine biosynthetic process / isoleucine biosynthetic process / NADP binding / magnesium ion binding / cytosol
Similarity search - Function
Ketol-acid reductoisomerase, prokaryotic / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Ketol-acid reductoisomerase, C-terminal domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(2S)-2-hydroxy-2-methyl-3-oxobutanoic acid / Ketol-acid reductoisomerase (NADP(+))
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLin, X. / Lonhienne, T. / Guddat, L.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210101802 Australia
CitationJournal: Acs Catalysis / Year: 2024
Title: Mapping of the Reaction Trajectory catalyzed by Class I Ketol-Acid Reductoisomerase
Authors: Lin, X. / Lonhienne, T. / Lv, Y. / Kurz, J. / McGeary, R. / Schenk, G. / Guddat, L.W.
History
DepositionMay 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ketol-acid reductoisomerase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1096
Polymers35,8681
Non-polymers2405
Water19811
1
A: Ketol-acid reductoisomerase (NADP(+))
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)433,30472
Polymers430,41912
Non-polymers2,88660
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area79960 Å2
ΔGint-963 kcal/mol
Surface area136600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.715, 130.715, 130.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-405-

CL

-
Components

#1: Protein Ketol-acid reductoisomerase (NADP(+)) / KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / ...KARI / Acetohydroxy-acid isomeroreductase / AHIR / Alpha-keto-beta-hydroxylacyl reductoisomerase / Ketol-acid reductoisomerase type 1 / Ketol-acid reductoisomerase type I


Mass: 35868.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Gene: ilvC, CJE0735 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5HVD9, ketol-acid reductoisomerase (NADP+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-X2X / (2S)-2-hydroxy-2-methyl-3-oxobutanoic acid


Mass: 132.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium acetate, 0.1 M BIS-TRIS pH=5.5 and 17 % w/v PEG10000
PH range: 5.5-7.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→46.21 Å / Num. obs: 7593 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 81.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.038 / Rrim(I) all: 0.078 / Net I/σ(I): 16.9
Reflection shellResolution: 3→3.18 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3 / Num. unique obs: 3286 / CC1/2: 0.918 / Rpim(I) all: 0.263 / Rrim(I) all: 0.542 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.34 Å / SU ML: 0.4325 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.8657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 755 9.95 %
Rwork0.2253 6836 -
obs0.2277 7591 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.45 Å2
Refinement stepCycle: LAST / Resolution: 3→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 13 11 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782435
X-RAY DIFFRACTIONf_angle_d0.84863297
X-RAY DIFFRACTIONf_chiral_restr0.0487377
X-RAY DIFFRACTIONf_plane_restr0.0054435
X-RAY DIFFRACTIONf_dihedral_angle_d16.5329864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.38841480.32141346X-RAY DIFFRACTION98.87
3.23-3.550.30821530.27411342X-RAY DIFFRACTION100
3.56-4.070.28841500.23881359X-RAY DIFFRACTION100
4.07-5.130.21581530.20951374X-RAY DIFFRACTION100
5.13-41.340.20911510.19541415X-RAY DIFFRACTION99.94

+
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