[English] 日本語
Yorodumi
- PDB-7toc: Crystal Structure of the Mitochondrial Ketol-acid Reductoisomeras... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7toc
TitleCrystal Structure of the Mitochondrial Ketol-acid Reductoisomerase IlvC from Candida auris
ComponentsKetol-acid reductoisomerase, mitochondrial
KeywordsISOMERASE / L-isoleucine biosynthesis / L-valine biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ketol-acid reductoisomerase (NADP+) / ketol-acid reductoisomerase activity / valine biosynthetic process / isoleucine biosynthetic process / isomerase activity / mitochondrion / metal ion binding
Similarity search - Function
Ketol-acid reductoisomerase, fungi / Ketol-acid reductoisomerase, C-terminal / Ketol-acid reductoisomerase / Ketol-acid reductoisomerase, N-terminal / Acetohydroxy acid isomeroreductase, catalytic domain / Acetohydroxy acid isomeroreductase, NADPH-binding domain / KARI N-terminal domain profile. / KARI C-terminal domain profile. / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETIC ACID / MALONATE ION / Chem-NDP / Ketol-acid reductoisomerase, mitochondrial
Similarity search - Component
Biological species[Candida] auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKim, Y. / Evdokimova, E. / Di, R. / Stogios, P. / Savchenko, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Mitochondrial Ketol-acid Reductoisomerase IlvC from Candida auris
Authors: Kim, Y. / Evdokimova, E. / Di, R. / Stogios, P. / Savchenko, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ketol-acid reductoisomerase, mitochondrial
B: Ketol-acid reductoisomerase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,84512
Polymers80,9332
Non-polymers1,91210
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16770 Å2
ΔGint-124 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.555, 145.555, 244.349
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ketol-acid reductoisomerase, mitochondrial / Acetohydroxy-acid reductoisomerase / Alpha-keto-beta-hydroxylacyl reductoisomerase


Mass: 40466.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] auris (fungus) / Gene: ilvC / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold
References: UniProt: A0A510NYT4, ketol-acid reductoisomerase (NADP+)

-
Non-polymers , 5 types, 76 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#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 interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Na Cacodylate pH6, 2M Na Malonate pH7.4, 2mM NADPH, 5mM MgCl2
PH range: 6-7.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 58168 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 58.96 Å2 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.037 / Rrim(I) all: 0.159 / Net I/σ(I): 23.4
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.238 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 2853 / CC1/2: 0.409 / Rpim(I) all: 0.611 / Rrim(I) all: 2.321 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha fold 2 model

Resolution: 2.43→41.12 Å / SU ML: 0.3424 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2086 2846 4.9 %
Rwork0.1796 55226 -
obs0.181 58072 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.23 Å2
Refinement stepCycle: LAST / Resolution: 2.43→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5646 0 122 66 5834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075890
X-RAY DIFFRACTIONf_angle_d0.87397988
X-RAY DIFFRACTIONf_chiral_restr0.0529858
X-RAY DIFFRACTIONf_plane_restr0.00851036
X-RAY DIFFRACTIONf_dihedral_angle_d8.5686870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.470.32721330.31872709X-RAY DIFFRACTION99.37
2.47-2.520.33371360.29622719X-RAY DIFFRACTION99.96
2.52-2.570.31561530.28322674X-RAY DIFFRACTION100
2.57-2.620.35591460.30352695X-RAY DIFFRACTION100
2.62-2.670.3361200.29592735X-RAY DIFFRACTION99.96
2.67-2.740.30281580.28912708X-RAY DIFFRACTION100
2.74-2.810.31351340.26542735X-RAY DIFFRACTION100
2.81-2.880.3321330.26642727X-RAY DIFFRACTION99.97
2.88-2.970.26971390.2472750X-RAY DIFFRACTION100
2.97-3.060.26151370.24312725X-RAY DIFFRACTION100
3.06-3.170.2851530.24252726X-RAY DIFFRACTION100
3.17-3.30.28821430.24542737X-RAY DIFFRACTION100
3.3-3.450.24911270.19912766X-RAY DIFFRACTION100
3.45-3.630.18921440.16952754X-RAY DIFFRACTION100
3.63-3.860.17761390.15692777X-RAY DIFFRACTION100
3.86-4.150.18171510.13872776X-RAY DIFFRACTION100
4.16-4.570.1381400.11382801X-RAY DIFFRACTION100
4.57-5.230.14391500.11742817X-RAY DIFFRACTION100
5.23-6.590.16431480.15212855X-RAY DIFFRACTION99.97
6.59-41.120.18611620.15263040X-RAY DIFFRACTION99.84
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)
19.105529654551.372850509321.050224702277.13371511765-0.3539311601639.362907353790.0773153297540.565534042289-0.403118818206-0.0523639833137-0.176016251082-0.6378262765280.4470197721791.18909772250.06361486995580.4949323957670.2962509057560.05413161430090.9087877526360.0315437656310.576243103758-10.5612025443-68.173077325-58.9591828597
23.279683962020.7545478534380.7932098713984.29435456790.67076242684.837828836840.2958493586460.783459369560.346011237018-0.653552375225-0.226725184928-0.0870393709849-0.653863877890.0869824800836-0.07566697928460.5738222069570.2059557757450.06393960394670.7240180676590.2067796812240.577429608783-19.1522395366-54.2978080487-61.796377484
32.52116012158-0.4551332761180.19089109011.41845001866-0.3254186727483.163621524210.09816504847080.4191540889460.3092117901040.05333209151730.2659374554270.271416520882-0.823309871879-0.670301644689-0.3109288696190.5001123087480.2333793321920.05159101615770.5793133803710.1518604988550.593409995853-25.8262564743-54.4933046405-49.1555709245
44.123751214660.715301788171.021385002010.7652785306410.5007298868714.05787268760.2400165880620.1236077482821.152107891720.369802067178-0.496975574923-0.118182248375-1.411772543550.3727379077110.3071611249451.13067846513-0.1582441033490.03961048308460.4286373607760.1636407855840.728247172681-8.30473525595-45.2733678839-33.6742370256
51.13313645032-0.138146733219-0.1776129846992.47445064466-0.3104432983162.795755456980.0358247214257-0.02575833262080.5020982083810.2737156717730.184714334056-0.183045466553-1.566415914880.350868565197-0.07788063795571.02593617125-0.1454396887990.07992728724730.409322639927-0.06865641480790.638459869352-9.71576691266-48.0428412943-21.7150294721
63.307665705380.1503268227821.887756170860.6905245190220.3257124560635.476599176950.2947693958361.507390666040.430656414658-0.1018774391040.0189262097220.088961161962-0.9502076165070.924643070115-0.3274542536340.955590635955-0.2416286101630.02825101832181.014238878860.2908277451750.698780290014-3.17223560931-45.7775410973-49.5577411348
73.374222053620.305880432946-1.472140703032.82416188872-3.674560878355.12832861792-0.2865404097670.437355234165-0.114861238424-0.3394994241090.00853220057324-0.278068560854-0.44184580571.292643622970.3254660086450.540299395433-0.261602016393-0.06762201155261.064571353680.06214703779140.5569529487565.23690346936-60.5069284185-30.1814738486
82.820279691492.187019535660.6020678769672.082041944820.3892863713770.195003621801-0.5451295610570.9185077266430.109553758236-0.1443353319960.532566704325-0.243249636467-0.4230610205490.6558646270450.01549269848130.575753945691-0.241867855618-0.1387088314461.25070552590.04986449670640.71971662592215.3913506391-60.2808301779-18.4275694041
95.72730922281-1.067778826421.123025831932.99285625265-0.8332117468014.94301246390.1304340284460.00960461955968-0.1206016543270.463122556756-0.145477741923-0.5623994727470.3950535665191.222855188040.02170891935590.393434412756-0.0719338999153-0.04955211169280.734627844447-0.05551494905940.5346221491293.5730362024-74.1877527582-3.5798907119
102.901527731191.121501823810.8530421087654.977593574081.600169133318.276610237330.200037410836-0.39248722146-0.135776844045-0.03245919040550.118993328395-0.117130324065-0.300233068760.287579748702-0.2844989909670.307369470581-0.0430398085362-0.001342130590660.556781709151-0.007778775877560.443013540407-6.97569084757-69.056116865-2.66520351621
112.71260894373-1.941123258983.728318662784.43640348896-1.318345777815.85887493251-0.0109573939133-0.515812840029-0.335119328590.07527742932590.252256966213-0.0809251266884-0.4120569019270.0606774907342-0.2350210113660.4298979808970.03025318155470.07266729669870.533627103363-0.03772565517640.562384984436-13.4251116424-70.31193815432.60768147118
122.919696806680.2617192207951.430150119845.06951232473-1.454418766484.466853887390.12692052805-0.7699330419540.5215857287751.15528490685-0.1451311879330.22058750609-1.138085973030.6768133741620.1291996839170.664214672237-0.236870353860.001838582752990.747953046821-0.1256178319610.440371221637-1.1715842741-59.84483841726.48162026101
132.81627497207-1.28766335218-0.1887418449341.71760741903-1.347334180361.83429248386-0.0143573964503-0.2721530036710.2040275433770.4272661779530.028410678348-0.2208904381-0.9965001065991.03448069197-0.03330691011080.611018333324-0.334868952852-0.02372140646230.780870118101-0.05037888666820.5442337893123.27436648643-59.2028823074-5.08210073391
143.337396653151.378962892773.341567380911.536687937681.804226936333.54878985530.108775251266-0.3202504741820.1267344374370.0224770883904-0.0276217656957-0.736810966492-0.908228016611.45118354004-0.09941979989350.422172982504-0.285524317232-0.04831476312311.073903024720.01472095897590.63760259207410.0326285777-64.956023014-9.28983547967
151.234567338340.263126425999-0.5215523694781.70791680522-0.697824308753.686313654540.131208431326-0.01784402413540.7599619134040.0524348065543-0.1106548235040.0160466306701-1.618027510820.1392427244460.124005012621.13807713711-0.02400527090840.1419179455410.413493118462-0.04623859597770.669307646382-12.1335013865-46.0794707349-23.1862423581
162.642013731040.9722955022311.169231398081.19358559131.086340594192.902592825710.1831403993160.3254978486780.5175818343140.307907315768-0.006360727597270.117660898419-1.632065370050.535612385882-0.1145772636010.962785583907-0.1855209840460.07421936392390.4849732947950.1037326161620.595421264381-5.5260864191-47.7020848248-32.2201564184
175.83650193864-0.309340924313.094632520152.63859249377-0.654522374256.405647397160.23529196345-1.164334410490.5236838638830.876661786424-0.02865312845440.179560740597-1.95440262859-0.564672140346-0.1519264651271.44801780512-0.02345085350540.1294003990.704649698644-0.1111441161250.643934407959-14.6899922167-46.2338401147-4.48638068576
185.175624995450.00961024461032-0.05118486397467.905929147323.600805793385.26616075110.083609231689-0.1544470591920.147175556440.7880981788630.1648825224460.2772442554-0.609870588013-0.798316668555-0.32928567610.7152468101640.3063962325090.06005905624590.7206490727340.1297580622340.553534858468-26.2538812379-55.8984047866-25.3015585183
191.36141141137-1.755271514771.129584358313.22282183571-1.216092726331.05883837299-0.501074833043-0.339669198415-0.1287382941880.6463470096580.7809605581740.555461161079-0.591549896111-0.996160720142-0.3169649612330.7042590658090.3919136538910.05821158073611.025366394790.1942550342090.63577901635-35.6992568375-51.7249756341-37.0213844342
203.34328857707-0.3998462328390.8683187581394.68390673341-1.702152000394.92901577380.1836932864590.476062758305-0.102369234779-0.307360448035-0.08655822003050.04713460746170.314078123974-0.283831755893-0.114336180050.3869402937910.145682391965-0.01735196378640.6163871165090.04598760859370.46783378201-21.9244542233-66.4833440025-53.2431739462
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 117 through 135 )BE117 - 13576 - 94
22chain 'B' and (resid 136 through 165 )BE136 - 16595 - 124
33chain 'B' and (resid 166 through 252 )BE166 - 252125 - 211
44chain 'B' and (resid 253 through 286 )BE253 - 286212 - 245
55chain 'B' and (resid 287 through 352 )BE287 - 352246 - 311
66chain 'B' and (resid 353 through 381 )BE353 - 381312 - 340
77chain 'B' and (resid 382 through 400 )BE382 - 400341 - 359
88chain 'A' and (resid 42 through 71 )AA42 - 711 - 30
99chain 'A' and (resid 72 through 91 )AA72 - 9131 - 50
1010chain 'A' and (resid 92 through 116 )AA92 - 11651 - 75
1111chain 'A' and (resid 117 through 135 )AA117 - 13576 - 94
1212chain 'A' and (resid 136 through 165 )AA136 - 16595 - 124
1313chain 'A' and (resid 166 through 226 )AA166 - 226125 - 185
1414chain 'A' and (resid 227 through 252 )AA227 - 252186 - 211
1515chain 'A' and (resid 253 through 295 )AA253 - 295212 - 254
1616chain 'A' and (resid 296 through 353 )AA296 - 353255 - 312
1717chain 'A' and (resid 354 through 381 )AA354 - 381313 - 340
1818chain 'A' and (resid 382 through 400 )AA382 - 400341 - 359
1919chain 'B' and (resid 42 through 71 )BE42 - 711 - 30
2020chain 'B' and (resid 72 through 116 )BE72 - 11631 - 75

+
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