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- PDB-7toc: Crystal Structure of the Mitochondrial Ketol-acid Reductoisomeras... -

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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 / L-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 / 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, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...Ketol-acid reductoisomerase, fungi / 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, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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+)

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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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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

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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

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