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- PDB-8ojq: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 T778 mu... -

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Basic information

Entry
Database: PDB / ID: 8ojq
TitleArabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 T778 mutant 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 / carbon fixation / apoplast / cellular response to phosphate starvation / photosynthesis / tricarboxylic acid cycle / chloroplast / protein tetramerization ...phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / carbon fixation / apoplast / cellular response to phosphate starvation / photosynthesis / tricarboxylic acid cycle / chloroplast / 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: 3.04938394081 Å
AuthorsHaesaerts, S. / Loris, R. / Larsen, P.
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 1.0Apr 3, 2024Provider: repository / Type: Initial release

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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)223,0104
Polymers222,8202
Non-polymers1902
Water46826
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)446,0218
Polymers445,6414
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)128.000, 159.840, 141.920
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
17GLNGLNTHRTHR(chain 'A' and (resid 33 through 121 or resid 137...AA885 - 916892 - 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
215GLNGLNTHRTHR(chain 'B' and (resid 33 or (resid 34 through 35...BB885 - 916892 - 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: 111410.219 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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.09M Sodium nitrate, 0.09 Sodium phosphate dibasic, 0.09M Ammonium sulfate, 0.1M MES monohydrate pH6.5, 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 9M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 3.04938394081→49.1888118125 Å / Num. obs: 55452 / % possible obs: 99.7 % / Redundancy: 14 % / Biso Wilson estimate: 114.907148133 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.89
Reflection shellResolution: 3.04938394081→3.15 Å / Rmerge(I) obs: 2.493 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 5360 / CC1/2: 0.444 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04938394081→49.1888118125 Å / SU ML: 0.390061057994 / Cross valid method: FREE R-VALUE / σ(F): 1.34366206061 / Phase error: 28.0674569207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.240217764959 2000 3.81199252849 %
Rwork0.20525535654 50466 -
obs0.206582212729 52466 93.4057325975 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.383983856 Å2
Refinement stepCycle: LAST / Resolution: 3.04938394081→49.1888118125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14386 0 10 26 14422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058360368119814732
X-RAY DIFFRACTIONf_angle_d0.81823477691719956
X-RAY DIFFRACTIONf_chiral_restr0.04724031512822205
X-RAY DIFFRACTIONf_plane_restr0.006176553821212590
X-RAY DIFFRACTIONf_dihedral_angle_d15.89139331478943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0494-3.12560.319028922823570.3155803618281430X-RAY DIFFRACTION37.5599898964
3.1256-3.21010.3107299418841100.3015660334432785X-RAY DIFFRACTION73.1430015159
3.2101-3.30460.3201551407171450.3114877232443664X-RAY DIFFRACTION96.2597927723
3.3046-3.41120.3157878894341510.284663971393800X-RAY DIFFRACTION99.9746963563
3.4112-3.53310.3330248143661510.2509734621023816X-RAY DIFFRACTION99.9747983871
3.5331-3.67450.2632455585141510.2373641314013834X-RAY DIFFRACTION99.9749121927
3.6745-3.84170.2833801525391520.2263518203783820X-RAY DIFFRACTION99.9748301032
3.8417-4.04410.2347278047451520.2170889382163828X-RAY DIFFRACTION100
4.0441-4.29740.2584472667311530.1859769834073848X-RAY DIFFRACTION100
4.2974-4.62890.2146109475481510.1748265875423842X-RAY DIFFRACTION100
4.6289-5.09430.2261042866851540.1678156601163892X-RAY DIFFRACTION100
5.0943-5.83050.2097952957951550.1936055003723894X-RAY DIFFRACTION100
5.8305-7.34190.2560623901011560.2220047143473933X-RAY DIFFRACTION100
7.3419-49.18881181250.2129477287441620.1904543959914080X-RAY DIFFRACTION99.6242367309
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)
10.06366150199430.106779313863-0.04236026131760.1429713116580.1347381300930.11435083885-0.0229711334703-0.615562506866-0.1087496742680.754059272597-0.03446272892830.56664764692-0.104435789618-0.211775353913-7.10672854726E-51.04096155273-0.2464438784220.1075592628891.153455284780.1289510301451.04755362613111.9731777147.8006018067173.651977892
20.865844893116-0.0934001834615-0.2941186466021.1269475079-0.1934600470320.3551220787280.0713478456588-0.036337257610.0101322848141-0.06616438106120.0181435912965-0.1423186394470.127870327674-0.009463635196197.48680680234E-60.738234564704-0.0492612035248-0.09412122081450.6773622140690.004385653845680.666169843138143.72593033164.4303813585147.714115942
31.019208746170.245681299039-0.2938336849110.2570546170250.1780627810480.3169440484670.0931732098572-0.237829760774-0.231795945060.143002573733-0.0345171674805-0.1103551389220.2393083131980.04659360999834.8403414378E-50.88069762928-0.0800240289144-0.2012365294160.7422282124850.2024495973270.876957306458135.68267641.6382731785163.784703925
40.03076947413690.135947232702-0.1073365242390.188166186097-0.09199786896950.08413297548080.5757256190270.8823953975970.0958581249429-0.685483050031-0.6551973867-0.1241838319650.044952308276-0.00282273141647-0.04718048347451.539316155010.5518588570090.260084157141.657391633650.3652648018731.29558328248148.40216287983.595055977763.9857452526
51.41794769293-0.794544171878-0.2090865302521.426071540610.08452114036470.4101049277360.3303039186370.355456993908-0.0105895371536-0.0122555040547-0.5237303110050.1274701277280.1396367243260.2307527135180.0001503665298730.9736659536660.1361069526720.02431891727281.00973039939-0.0186367003840.850519035829137.98858618464.354342779291.7033843304
60.527919537045-0.03198587567870.2002849447960.263343917909-0.002272492739990.0607423463060.5541501574711.050175415920.00463681379309-0.403158006978-0.598364865536-0.302796393040.237036243315-0.223242676288-0.02338630574631.117468722880.5622879144290.1332492046861.50327841210.1100769744791.0100510581157.92053767355.471710324183.2452844577
70.4167643421050.162156619247-0.2364062093970.24868354763-0.380592354470.4059569771430.3215740604110.8884432361660.0762700359026-0.403875365976-0.520928820391-0.6103970349260.2037667925660.351719134458-0.03464074367471.191986278520.5561955655590.4867436490041.931816954640.4722710487821.57850168538168.26275031873.9195443767.7184468715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 647 )
3X-RAY DIFFRACTION3chain 'A' and (resid 648 through 967 )
4X-RAY DIFFRACTION4chain 'B' and (resid 33 through 221 )
5X-RAY DIFFRACTION5chain 'B' and (resid 222 through 519 )
6X-RAY DIFFRACTION6chain 'B' and (resid 520 through 679 )
7X-RAY DIFFRACTION7chain 'B' and (resid 680 through 967 )

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