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- PDB-8ojf: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 with bo... -

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Basic information

Entry
Database: PDB / ID: 8ojf
TitleArabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 with bound phosphate
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
PHOSPHATE ION / Phosphoenolpyruvate carboxylase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0368376252 Å
AuthorsHaesaerts, S. / Loris, R. / 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. / Haesaerts, S. / Frausto, K. / O'Leary, S. / Loris, R. / Larsen, P.B.
History
DepositionMar 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)223,1527
Polymers222,7962
Non-polymers3565
Water32418
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)446,30414
Polymers445,5934
Non-polymers71210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)127.220, 158.170, 141.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
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
11TYRTYRLYSLYS(chain 'A' and (resid 33 through 121 or resid 137...AA33 - 12140 - 128
12SERSERTHRTHR(chain 'A' and (resid 33 through 121 or resid 137...AA137 - 300144 - 307
13ASPASPALAALA(chain 'A' and (resid 33 through 121 or resid 137...AA302 - 604309 - 611
14LEULEUPROPRO(chain 'A' and (resid 33 through 121 or resid 137...AA607 - 756614 - 763
15GLYGLYILEILE(chain 'A' and (resid 33 through 121 or resid 137...AA764 - 794771 - 801
16HISHISHISHIS(chain 'A' and (resid 33 through 121 or resid 137...AA796 - 873803 - 880
17LEULEUTHRTHR(chain 'A' and (resid 33 through 121 or resid 137...AA887 - 916894 - 923
18LYSLYSGLYGLY(chain 'A' and (resid 33 through 121 or resid 137...AA930 - 967937 - 974
29TYRTYRLYSLYS(chain 'B' and (resid 33 or (resid 34 through 35...BB33 - 12140 - 128
210SERSERTHRTHR(chain 'B' and (resid 33 or (resid 34 through 35...BB137 - 300144 - 307
211ASPASPALAALA(chain 'B' and (resid 33 or (resid 34 through 35...BB302 - 604309 - 611
212LEULEUPROPRO(chain 'B' and (resid 33 or (resid 34 through 35...BB607 - 756614 - 763
213GLYGLYILEILE(chain 'B' and (resid 33 or (resid 34 through 35...BB764 - 794771 - 801
214HISHISHISHIS(chain 'B' and (resid 33 or (resid 34 through 35...BB796 - 873803 - 880
215LEULEUTHRTHR(chain 'B' and (resid 33 or (resid 34 through 35...BB887 - 916894 - 923
216LYSLYSGLYGLY(chain 'B' and (resid 33 or (resid 34 through 35...BB930 - 967937 - 974

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Components

#1: Protein Phosphoenolpyruvate carboxylase 1 / AtPPC1 / PEPC 1 / PEPCase 1 / 107-kDa PEPC polypeptide


Mass: 111398.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPC1, p107, At1g53310, F12M16.21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9MAH0, phosphoenolpyruvate carboxylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.09M Sodium nitrate, 0.09 Sodium phosphate dibasic, 0.09M Ammonium sulfate, 0.1M MES monohydrate pH 6.5, 20% v/v Ethylene glycol; 10 % w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.981 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 3.029→48.8 Å / Num. obs: 55586 / % possible obs: 99.8 % / Redundancy: 13.74 % / Biso Wilson estimate: 114.572419455 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.152 / Net I/σ(I): 10.86
Reflection shellResolution: 3.029→3.22 Å / Redundancy: 13.96 % / Rmerge(I) obs: 2.63 / Num. unique obs: 8756 / CC1/2: 0.36 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.0368376252→48.7063417119 Å / SU ML: 0.48126573983 / Cross valid method: FREE R-VALUE / σ(F): 1.33789407038 / Phase error: 28.2293480275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242683220805 2774 5.00252470605 %
Rwork0.202838068279 52678 -
obs0.20485384429 55452 99.7391945609 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.299495629 Å2
Refinement stepCycle: LAST / Resolution: 3.0368376252→48.7063417119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14334 0 17 18 14369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062202634969814683
X-RAY DIFFRACTIONf_angle_d0.87833913622819900
X-RAY DIFFRACTIONf_chiral_restr0.04965295163662203
X-RAY DIFFRACTIONf_plane_restr0.005837440755152584
X-RAY DIFFRACTIONf_dihedral_angle_d15.6853140788898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0368376252-3.08920.4348291215641320.4000230171422485X-RAY DIFFRACTION95.3022578296
3.0892-3.14540.409855029961360.370324805682587X-RAY DIFFRACTION99.9632892805
3.1454-3.20580.3205305494711380.3248162302912614X-RAY DIFFRACTION99.9636759898
3.2058-3.27130.3641104269271380.3014802258382616X-RAY DIFFRACTION100
3.2713-3.34240.3268804970741370.2913330665122604X-RAY DIFFRACTION99.9635302699
3.3424-3.42010.3019966148691360.286222278282590X-RAY DIFFRACTION100
3.4201-3.50560.3212963071541380.2809637830522629X-RAY DIFFRACTION99.9638728324
3.5056-3.60040.2694421344981380.2558574109392612X-RAY DIFFRACTION100
3.6004-3.70630.2730428952961380.225449651642615X-RAY DIFFRACTION99.9274047187
3.7063-3.82590.3002625208741370.2298323793832612X-RAY DIFFRACTION100
3.8259-3.96250.2558711786271380.2132403314332628X-RAY DIFFRACTION100
3.9625-4.12110.256285255111380.1920977249522623X-RAY DIFFRACTION100
4.1211-4.30860.2026299139321390.1782960590092630X-RAY DIFFRACTION100
4.3086-4.53560.2151336973481390.1691602080032647X-RAY DIFFRACTION100
4.5356-4.81950.1926962775431390.1595377773142636X-RAY DIFFRACTION100
4.8195-5.19120.2379223714921400.1685462563982651X-RAY DIFFRACTION100
5.1912-5.71290.260670688191400.1947200577082664X-RAY DIFFRACTION100
5.7129-6.53790.2560988177811410.2059604169722690X-RAY DIFFRACTION100
6.5379-8.23060.1996670839761430.1821747239392717X-RAY DIFFRACTION100
8.2306-48.706330.2151629843381490.1843896002712828X-RAY DIFFRACTION99.6652159357
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)
10.758680586947-0.278862613022-0.331058694811.069028019380.08593641819060.515414329535-0.0153827459458-0.383670340918-0.06439519730510.342005351926-0.04347296640920.2388660393030.0856043055645-0.07089810320490.06109088343311.00626508959-0.0712504438756-0.04739082579320.9547515992640.06452616079940.831327656663124.75030572158.5035908194167.577170789
21.20245593669-0.189854884807-0.3058028231672.068933602330.1845575098630.4595728835340.06530578637190.0050168992269-0.0716678148276-0.0427060054845-0.00223233102792-0.1729019356990.104871965551-0.0481761264951-0.05259099478970.799197204957-0.0450777425045-0.05995112832890.774930109950.02219997733750.774059135141146.93940514763.0337879852144.136722939
32.585923404540.01124880688450.2101884975611.27023502032-0.1282354400840.9358619730490.0927898243136-0.210966281754-0.467129178890.249821995066-0.0915476149715-0.182327445830.3930960162350.1382593175110.03091842946690.998275744131-0.0723055014717-0.14975248840.8078354240810.2164050965051.04710297674132.7642851636.809126951162.928850831
40.547093567729-0.502056377699-0.3484633659110.806981408652-0.2831289694351.066481669890.5716457458260.9630381525290.201537394962-1.02207612412-0.64419511184-0.386442725653-0.1230356967340.3601012205110.09723940813981.657529820320.3959084767470.1677374948681.938302245170.353137724861.47111760556147.58679203783.243973845163.6149062779
52.17886047227-1.158154782970.2513006910452.00270688285-0.4635865012661.227860527860.2899170583210.309495508511-0.1273079963810.0677955926901-0.4307492079370.04793182518630.1657825999470.1829265248120.1317566955481.137472672520.02957457726760.0004506603393091.1546205927-0.04783131503221.02335932462142.16474576461.423524853890.9584363857
60.6741115991840.265274388888-0.03663507833730.673365828992-0.7865187325541.05834588840.2758855133880.9234672775990.229973876235-0.566069703956-0.304382758096-1.008255731090.2575702121580.691017266010.001062081079331.369079933460.403580059470.3525511889262.214729741430.2273556964661.78997850844165.2872472970.237593888668.5947576147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 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 33 through 221 )
5X-RAY DIFFRACTION5chain 'B' and (resid 222 through 605 )
6X-RAY DIFFRACTION6chain 'B' and (resid 606 through 967 )

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