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- PDB-8qx1: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 R886G m... -

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Basic information

Entry
Database: PDB / ID: 8qx1
TitleArabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 R886G mutant with bound malate
ComponentsPhosphoenolpyruvate carboxylase 1
KeywordsPLANT PROTEIN / Phosphoenolpyruvate carboxylase / Citric acid cycle / TCA cycle / photosynthesis
Function / homology
Function and homology information


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / apoplast / carbon fixation / cellular response to phosphate starvation / photosynthesis / tricarboxylic acid cycle / protein tetramerization / nucleus / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / DI(HYDROXYETHYL)ETHER / Phosphoenolpyruvate carboxylase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9445137477 Å
AuthorsLoris, R. / Haesaerts, S. / Larsen, P.B.
Funding support United States, Belgium, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2021-67014-34888 United States
Research Foundation - Flanders (FWO)G011420N Belgium
CitationJournal: To Be Published
Title: Amino acid changes that deregulate PHOSPHOENOLPYRUVATE CARBOXYLASE in plants
Authors: Meyer, T.J. / Sheng, J. / Haesearts, S. / Fausto, K. / O'Leary, S. / Loris, R. / Larsen, P.B.
History
DepositionOct 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxylase 1
B: Phosphoenolpyruvate carboxylase 1
C: Phosphoenolpyruvate carboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,41928
Polymers333,8943
Non-polymers2,52525
Water1,892105
1
A: Phosphoenolpyruvate carboxylase 1
B: Phosphoenolpyruvate carboxylase 1
hetero molecules

A: Phosphoenolpyruvate carboxylase 1
B: Phosphoenolpyruvate carboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,99332
Polymers445,1924
Non-polymers2,80128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
2
C: Phosphoenolpyruvate carboxylase 1
hetero molecules

C: Phosphoenolpyruvate carboxylase 1
hetero molecules

C: Phosphoenolpyruvate carboxylase 1
hetero molecules

C: Phosphoenolpyruvate carboxylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,69148
Polymers445,1924
Non-polymers4,49844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Unit cell
Length a, b, c (Å)242.380, 242.380, 396.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

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
11LYSLYSGLUGLU(chain 'A' and (resid 6 or (resid 8 through 21...AA8 - 6815 - 75
12HISHISSERSER(chain 'A' and (resid 6 or (resid 8 through 21...AA71 - 15378 - 160
13GLUGLULEULEU(chain 'A' and (resid 6 or (resid 8 through 21...AA156 - 209163 - 216
14ALAALAILEILE(chain 'A' and (resid 6 or (resid 8 through 21...AA212 - 226219 - 233
15THRTHRTHRTHR(chain 'A' and (resid 6 or (resid 8 through 21...AA229 - 296236 - 303
16VALVALILEILE(chain 'A' and (resid 6 or (resid 8 through 21...AA299 - 319306 - 326
17LEULEUASNASN(chain 'A' and (resid 6 or (resid 8 through 21...AA322 - 345329 - 352
18ALAALAPHEPHE(chain 'A' and (resid 6 or (resid 8 through 21...AA351 - 357358 - 364
19SERSERTHRTHR(chain 'A' and (resid 6 or (resid 8 through 21...AA360 - 381367 - 388
110ARGARGGLYGLY(chain 'A' and (resid 6 or (resid 8 through 21...AA384 - 492391 - 499
111PROPROTYRTYR(chain 'A' and (resid 6 or (resid 8 through 21...AA495 - 583502 - 590
112ARGARGILEILE(chain 'A' and (resid 6 or (resid 8 through 21...AA586 - 595593 - 602
113SERSERALAALA(chain 'A' and (resid 6 or (resid 8 through 21...AA598 - 604605 - 611
114LEULEUHISHIS(chain 'A' and (resid 6 or (resid 8 through 21...AA607 - 635614 - 642
115GLYGLYGLYGLY(chain 'A' and (resid 6 or (resid 8 through 21...AA638 - 678645 - 685
116HISHISGLUGLU(chain 'A' and (resid 6 or (resid 8 through 21...AA681 - 708688 - 715
117ALAALAPROPRO(chain 'A' and (resid 6 or (resid 8 through 21...AA711 - 756718 - 763
118GLYGLYHISHIS(chain 'A' and (resid 6 or (resid 8 through 21...AA763 - 920770 - 927
21LYSLYSGLUGLU(chain 'B' and (resid 6 or (resid 8 through 21...BB8 - 6815 - 75
22HISHISSERSER(chain 'B' and (resid 6 or (resid 8 through 21...BB71 - 15378 - 160
23GLUGLULEULEU(chain 'B' and (resid 6 or (resid 8 through 21...BB156 - 209163 - 216
24ALAALAILEILE(chain 'B' and (resid 6 or (resid 8 through 21...BB212 - 226219 - 233
25THRTHRTHRTHR(chain 'B' and (resid 6 or (resid 8 through 21...BB229 - 296236 - 303
26VALVALILEILE(chain 'B' and (resid 6 or (resid 8 through 21...BB299 - 319306 - 326
27LEULEUASNASN(chain 'B' and (resid 6 or (resid 8 through 21...BB322 - 345329 - 352
28ALAALAPHEPHE(chain 'B' and (resid 6 or (resid 8 through 21...BB351 - 357358 - 364
29SERSERTHRTHR(chain 'B' and (resid 6 or (resid 8 through 21...BB360 - 381367 - 388
210ARGARGGLYGLY(chain 'B' and (resid 6 or (resid 8 through 21...BB384 - 492391 - 499
211PROPROTYRTYR(chain 'B' and (resid 6 or (resid 8 through 21...BB495 - 583502 - 590
212ARGARGILEILE(chain 'B' and (resid 6 or (resid 8 through 21...BB586 - 595593 - 602
213SERSERALAALA(chain 'B' and (resid 6 or (resid 8 through 21...BB598 - 604605 - 611
214LEULEUHISHIS(chain 'B' and (resid 6 or (resid 8 through 21...BB607 - 635614 - 642
215GLYGLYGLYGLY(chain 'B' and (resid 6 or (resid 8 through 21...BB638 - 678645 - 685
216HISHISGLUGLU(chain 'B' and (resid 6 or (resid 8 through 21...BB681 - 708688 - 715
217ALAALAPROPRO(chain 'B' and (resid 6 or (resid 8 through 21...BB711 - 756718 - 763
218GLYGLYHISHIS(chain 'B' and (resid 6 or (resid 8 through 21...BB763 - 920770 - 927
31LYSLYSGLUGLU(chain 'C' and ((resid 6 and (name N or name...CC8 - 6815 - 75
32HISHISSERSER(chain 'C' and ((resid 6 and (name N or name...CC71 - 15378 - 160
33GLUGLULEULEU(chain 'C' and ((resid 6 and (name N or name...CC156 - 209163 - 216
34ALAALAILEILE(chain 'C' and ((resid 6 and (name N or name...CC212 - 226219 - 233
35THRTHRTHRTHR(chain 'C' and ((resid 6 and (name N or name...CC229 - 296236 - 303
36VALVALILEILE(chain 'C' and ((resid 6 and (name N or name...CC299 - 319306 - 326
37LEULEUASNASN(chain 'C' and ((resid 6 and (name N or name...CC322 - 345329 - 352
38ALAALAPHEPHE(chain 'C' and ((resid 6 and (name N or name...CC351 - 357358 - 364
39SERSERTHRTHR(chain 'C' and ((resid 6 and (name N or name...CC360 - 381367 - 388
310ARGARGGLYGLY(chain 'C' and ((resid 6 and (name N or name...CC384 - 492391 - 499
311PROPROTYRTYR(chain 'C' and ((resid 6 and (name N or name...CC495 - 583502 - 590
312ARGARGILEILE(chain 'C' and ((resid 6 and (name N or name...CC586 - 595593 - 602
313SERSERALAALA(chain 'C' and ((resid 6 and (name N or name...CC598 - 604605 - 611
314LEULEUHISHIS(chain 'C' and ((resid 6 and (name N or name...CC607 - 635614 - 642
315GLYGLYGLYGLY(chain 'C' and ((resid 6 and (name N or name...CC638 - 678645 - 685
316HISHISGLUGLU(chain 'C' and ((resid 6 and (name N or name...CC681 - 708688 - 715
317ALAALAPROPRO(chain 'C' and ((resid 6 and (name N or name...CC711 - 756718 - 763
318GLYGLYHISHIS(chain 'C' and ((resid 6 and (name N or name...CC763 - 920770 - 927

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Components

#1: Protein Phosphoenolpyruvate carboxylase 1


Mass: 111298.023 Da / Num. of mol.: 3 / Mutation: R886G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9MAH0
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.48 Å3/Da / Density % sol: 72.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 30% w/v PEG400; 0.1M MES pH6.5; 0,1M NaAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.94→48.12 Å / Num. obs: 123364 / % possible obs: 99.6 % / Redundancy: 23.82 % / Biso Wilson estimate: 76.1709538037 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.298 / Net I/σ(I): 10.13
Reflection shellResolution: 2.94→3.12 Å / Rmerge(I) obs: 3.435 / Num. unique obs: 19319 / CC1/2: 0.803

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9445137477→48.1168917258 Å / SU ML: 0.420464644818 / Cross valid method: FREE R-VALUE / σ(F): 1.33645412166 / Phase error: 31.7964135912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241772889651 6135 5.00179363423 %
Rwork0.203169701804 116521 -
obs0.205129681444 122656 99.2041410547 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.1228405692 Å2
Refinement stepCycle: LAST / Resolution: 2.9445137477→48.1168917258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21803 0 126 105 22034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047834701121122481
X-RAY DIFFRACTIONf_angle_d0.71480955296430497
X-RAY DIFFRACTIONf_chiral_restr0.0431320493553431
X-RAY DIFFRACTIONf_plane_restr0.006063407194173962
X-RAY DIFFRACTIONf_dihedral_angle_d12.531731675413512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.944515-2.9780.4651371608271780.3960437040693368X-RAY DIFFRACTION86.5934065934
2.978-3.0130.3677763915272010.3343938383033831X-RAY DIFFRACTION99.703264095
3.013-3.04970.3727521127952030.3238841842473851X-RAY DIFFRACTION99.8522167488
3.0497-3.08830.351133702962040.3301348176813853X-RAY DIFFRACTION99.6805896806
3.0883-3.1290.3515812275382040.3201739471163878X-RAY DIFFRACTION99.5366983663
3.129-3.17180.3457643491832050.3083228525343876X-RAY DIFFRACTION99.8287671233
3.1718-3.21710.3414194179732010.3013998442653846X-RAY DIFFRACTION99.8027127004
3.2171-3.26510.3043011042792050.2705593602663881X-RAY DIFFRACTION99.7802197802
3.2651-3.31610.3056043226172050.2546864809873883X-RAY DIFFRACTION99.5373752131
3.3161-3.37050.3135431296622030.2468464334193861X-RAY DIFFRACTION99.8525798526
3.3705-3.42860.2910549660992040.2362155918783877X-RAY DIFFRACTION99.8043531426
3.4286-3.49090.2515720208322040.224834488913883X-RAY DIFFRACTION99.7072456697
3.4909-3.55810.263917398542020.2115750088433847X-RAY DIFFRACTION99.5818986719
3.5581-3.63070.2806068869222050.2201023866083895X-RAY DIFFRACTION99.6839290056
3.6307-3.70960.2895383783742040.2052812239043872X-RAY DIFFRACTION99.7308539271
3.7096-3.79580.2609462872952050.1922290063243904X-RAY DIFFRACTION99.7088085416
3.7958-3.89070.2279351456132040.1924303192023871X-RAY DIFFRACTION99.6819960861
3.8907-3.99590.2285703266652060.1784702387613906X-RAY DIFFRACTION99.7573993207
3.9959-4.11340.2345745149872040.1742529151373886X-RAY DIFFRACTION99.8047828209
4.1134-4.24610.1990810538152040.1719375395163889X-RAY DIFFRACTION99.6833901607
4.2461-4.39770.2043891808472070.1577652753513923X-RAY DIFFRACTION99.8307952623
4.3977-4.57370.1937034310012060.1554159270323904X-RAY DIFFRACTION99.8057309373
4.5737-4.78170.1811142152732060.1487942912183905X-RAY DIFFRACTION99.5399515738
4.7817-5.03350.1951251409092070.1606825755423919X-RAY DIFFRACTION99.8306315025
5.0335-5.34850.2104475465652070.1671446483883937X-RAY DIFFRACTION99.7112608277
5.3485-5.76080.2291401534682070.1857865132983921X-RAY DIFFRACTION99.758337361
5.7608-6.33940.2493445727972100.2059738995493974X-RAY DIFFRACTION99.8568019093
6.3394-7.2540.2572892247072100.2022342093723979X-RAY DIFFRACTION99.8093876579
7.254-9.12910.1940474101212100.1786048105354016X-RAY DIFFRACTION99.740382346
9.1291-48.1150.2068099950092140.1997903309744085X-RAY DIFFRACTION97.0648001806
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)
12.40090628089-1.25230719068-0.5067456708532.157836314690.4757810950242.38809914486-0.149474271966-0.2052922227910.00401939202010.3865785683480.1119046591820.35010323198-0.49364691894-1.174803077070.04438710407230.9823347407530.1499175382680.04442157456730.9826629304360.03344956992520.5767886243574.186820446797.0811002498302.682480997
20.829758137005-0.242088306151-0.04214046982820.890577549376-0.3579893272481.891691936180.0183408151791-0.1580339250580.1202446723320.2934494212270.111359297851-0.21150069132-0.9657830497520.00136486674695-0.0773259932610.944879803224-0.198316392810.04879381238980.337295076469-0.04728474767780.6721744853102.689664169101.296384543289.851122675
32.07443466794-0.729395156219-0.8306022384392.018432153481.254199215023.238166879770.06922081180090.0232406520120.392037253454-0.07906975610630.1588937905980.159366684504-0.985417065122-0.66504769358-0.1505680799140.9316103007570.3647820073260.05362642407050.9603813004510.04310088589750.55878940639869.5792378617106.769658792281.360109325
40.730440945725-0.816484313985-0.1899040764422.460126800270.3263049447541.852507303940.0123952728545-0.11863273398-0.1251095443590.51257633203-0.0842652262040.221254895108-0.14662042726-0.1918995649650.05416826089690.727516422354-0.244011808990.03538685181640.594107888584-0.001479468071660.57471527146697.130946873474.3490532874328.568656992
50.996682099737-0.1034968137940.3073203766820.7988063239110.1275020018361.903854855660.1930447266780.1921100492660.1608542998630.268974022643-0.22182608602-0.0839197055133-0.7901984629820.1584117057170.07239718489831.41895366173-0.2495671761050.07355896429950.568892214601-0.03395797228690.604829723222100.714718694103.109098955342.134767241
61.27354306196-0.935046580026-1.027538169451.488386875810.9607177671284.007214448920.157931319949-0.2971639514880.0979517151670.7768999167320.0263359426875-0.229046806062-0.08342468363440.320575484077-0.1558896019211.03452784217-0.290021950684-0.09274146415610.469252515237-0.01818276834890.602304633298106.71411637669.9343586688350.050734791
71.760245035-1.704057585960.8122872113114.27868072812-1.724634489512.76078222620.0526140415380.0140848911430.295480959387-0.00966291530374-0.0841758887895-0.187731804501-0.27969997792-0.06896883747130.04290195958760.3907635718330.002074683374310.06956194294730.373858625415-0.06941603985050.379918241873145.416321295169.376063354214.20788731
80.288747789987-0.7197079598561.138825050712.99835141047-2.652063204824.266489986180.118473650208-0.124591682159-0.07020774253560.06908077331040.1630894263690.2202385260180.150492445772-0.142634380477-0.198747118890.372487604162-0.0003491575356850.008858206768190.457271435007-0.0996169907490.386410705954143.327958588156.455462447205.293463712
90.3208872904490.116019291975-0.5369913425490.558515384380.1064159183762.541029600460.0561592479751-0.0624021381644-0.1815883743290.1412375136470.02355926613620.04300466791640.546063244648-0.280391730359-0.06000926794370.548814658481-0.0263887237746-0.06272932052060.4651195428910.06099053068890.56297108013141.030934099139.715326465226.523301052
102.18558151438-0.6166850004821.026834871682.0494400022-0.6105628601714.19759406721-0.0158388848978-0.3961851336360.02219935906080.2956432228810.1429079737610.351733582307-0.727974580471-0.810411090118-0.114275094380.540620648240.1047139558720.1557492344240.52125862274-0.00957879106890.502521927748133.952607433173.269000723230.160778822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 221 )
2X-RAY DIFFRACTION2chain 'A' and (resid 222 through 706 )
3X-RAY DIFFRACTION3chain 'A' and (resid 707 through 967 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 222 )
5X-RAY DIFFRACTION5chain 'B' and (resid 223 through 706 )
6X-RAY DIFFRACTION6chain 'B' and (resid 707 through 967 )
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 179 )
8X-RAY DIFFRACTION8chain 'C' and (resid 180 through 266 )
9X-RAY DIFFRACTION9chain 'C' and (resid 267 through 728 )
10X-RAY DIFFRACTION10chain 'C' and (resid 729 through 967 )

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