[English] 日本語
Yorodumi
- PDB-8qtm: Arabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 G678S m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qtm
TitleArabidopsis thaliana Phosphoenolpyruvate carboxylase PPC1 G678S 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: 3.0920328441 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 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)336,17324
Polymers334,2853
Non-polymers1,88821
Water2,288127
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)447,45222
Polymers445,7134
Non-polymers1,73918
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)449,78852
Polymers445,7134
Non-polymers4,07548
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)242.871, 242.871, 396.113
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
11LYSLYSTHRTHR(chain 'A' and (resid 6 or resid 8 through 76...AA8 - 14215 - 149
12LYSLYSVALVAL(chain 'A' and (resid 6 or resid 8 through 76...AA144 - 178151 - 185
13ARGARGGLUGLU(chain 'A' and (resid 6 or resid 8 through 76...AA180 - 320187 - 327
14LEULEUSERSER(chain 'A' and (resid 6 or resid 8 through 76...AA322 - 346329 - 353
15ALAALAILEILE(chain 'A' and (resid 6 or resid 8 through 76...AA351 - 595358 - 602
16SERSERHISHIS(chain 'A' and (resid 6 or resid 8 through 76...AA598 - 635605 - 642
17GLYGLYTRPTRP(chain 'A' and (resid 6 or resid 8 through 76...AA638 - 709645 - 716
18ALAALALYSLYS(chain 'A' and (resid 6 or resid 8 through 76...AA711 - 758718 - 765
19GLYGLYLEULEU(chain 'A' and (resid 6 or resid 8 through 76...AA763 - 887770 - 894
110LEULEULYSLYS(chain 'A' and (resid 6 or resid 8 through 76...AA889 - 923896 - 930
111GLYGLYGLYGLY(chain 'A' and (resid 6 or resid 8 through 76...AA947 - 967954 - 974
212LYSLYSTHRTHR(chain 'B' and ((resid 6 and (name N or name...BB8 - 14215 - 149
213LYSLYSVALVAL(chain 'B' and ((resid 6 and (name N or name...BB144 - 178151 - 185
214ARGARGGLUGLU(chain 'B' and ((resid 6 and (name N or name...BB180 - 320187 - 327
215LEULEUSERSER(chain 'B' and ((resid 6 and (name N or name...BB322 - 346329 - 353
216ALAALAILEILE(chain 'B' and ((resid 6 and (name N or name...BB351 - 595358 - 602
217SERSERHISHIS(chain 'B' and ((resid 6 and (name N or name...BB598 - 635605 - 642
218GLYGLYTRPTRP(chain 'B' and ((resid 6 and (name N or name...BB638 - 709645 - 716
219ALAALALYSLYS(chain 'B' and ((resid 6 and (name N or name...BB711 - 758718 - 765
220GLYGLYLEULEU(chain 'B' and ((resid 6 and (name N or name...BB763 - 887770 - 894
221LEULEULYSLYS(chain 'B' and ((resid 6 and (name N or name...BB889 - 923896 - 930
222GLYGLYGLYGLY(chain 'B' and ((resid 6 and (name N or name...BB947 - 967954 - 974
323LYSLYSTHRTHR(chain 'C' and ((resid 6 and (name N or name...CC8 - 14215 - 149
324LYSLYSVALVAL(chain 'C' and ((resid 6 and (name N or name...CC144 - 178151 - 185
325ARGARGGLUGLU(chain 'C' and ((resid 6 and (name N or name...CC180 - 320187 - 327
326LEULEUSERSER(chain 'C' and ((resid 6 and (name N or name...CC322 - 346329 - 353
327ALAALAILEILE(chain 'C' and ((resid 6 and (name N or name...CC351 - 595358 - 602
328SERSERHISHIS(chain 'C' and ((resid 6 and (name N or name...CC598 - 635605 - 642
329GLYGLYTRPTRP(chain 'C' and ((resid 6 and (name N or name...CC638 - 709645 - 716
330ALAALALYSLYS(chain 'C' and ((resid 6 and (name N or name...CC711 - 758718 - 765
331GLYGLYLEULEU(chain 'C' and ((resid 6 and (name N or name...CC763 - 887770 - 894
332LEULEULYSLYS(chain 'C' and ((resid 6 and (name N or name...CC889 - 923896 - 930
333GLYGLYGLYGLY(chain 'C' and ((resid 6 and (name N or name...CC947 - 967954 - 974

-
Components

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


Mass: 111428.188 Da / Num. of mol.: 3 / Mutation: G678S
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-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


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


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M Hepes pH7.5; 0.2M MgCl2; 30% PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980114 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: 0.980114 Å / Relative weight: 1
ReflectionResolution: 3.092→49.5604 Å / Num. obs: 100172 / % possible obs: 93.2509 % / Redundancy: 25.4 % / Biso Wilson estimate: 78.5231297533 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.28 / Net I/σ(I): 8.16
Reflection shellResolution: 3.092→3.209 Å / Rmerge(I) obs: 3.357 / Num. unique obs: 10843 / CC1/2: 0.6347

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.11.1_2575refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.0920328441→49.5603860786 Å / SU ML: 0.333410108862 / Cross valid method: FREE R-VALUE / σ(F): 1.34759131961 / Phase error: 32.4263448171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252531051454 1998 1.99829974496 %
Rwork0.202636654183 97987 -
obs0.20362961591 99985 93.076837147 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.0567969531 Å2
Refinement stepCycle: LAST / Resolution: 3.0920328441→49.5603860786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22253 0 100 127 22480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010024953338622924
X-RAY DIFFRACTIONf_angle_d1.0676137692731099
X-RAY DIFFRACTIONf_chiral_restr0.05471457413083488
X-RAY DIFFRACTIONf_plane_restr0.007272862754284045
X-RAY DIFFRACTIONf_dihedral_angle_d13.527706029113856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.095-3.16930.408248302039550.3399915440952712X-RAY DIFFRACTION36.5232312566
3.1693-3.2550.3422326206051100.3029471326795392X-RAY DIFFRACTION72.6144912234
3.255-3.35080.3488156720931460.2759831221157150X-RAY DIFFRACTION95.7857424183
3.3508-3.45890.2933059895911510.2678399815467425X-RAY DIFFRACTION99.6973285959
3.4589-3.58250.2562411238521520.2413107716257430X-RAY DIFFRACTION99.9077612334
3.5825-3.72590.286295109081510.2301889971457471X-RAY DIFFRACTION99.9344434247
3.7259-3.89540.2450791362971530.1983243106777448X-RAY DIFFRACTION99.8817345598
3.8954-4.10070.2436974616641520.1831125912567479X-RAY DIFFRACTION99.9345206915
4.1007-4.35750.2786671277131520.1757175834887495X-RAY DIFFRACTION99.9477192524
4.3575-4.69370.1895369321991530.1654145382847508X-RAY DIFFRACTION99.8956839223
4.6937-5.16560.2319834002941530.1638532124357517X-RAY DIFFRACTION99.8048145738
5.1656-5.9120.2478078376591550.1910461109527556X-RAY DIFFRACTION99.7155049787
5.912-7.44440.2469324682341550.2211930912947622X-RAY DIFFRACTION99.8459365772
7.4444-49.50.2296672212651600.1842922658297782X-RAY DIFFRACTION98.5237563578
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)
12.65757047545-0.887319093394-0.4264612130681.725927229680.4951565469812.217877357640.0162136224086-0.314331083380.1359109936010.4029302912550.04333644723410.232061638957-0.772714596392-1.02347625564-0.04597943693621.066817910530.104988431577-0.0155497878340.733881384349-0.005427339262860.45112945249177.694190504797.9676761356302.617030448
20.627570888949-0.0430412389384-0.1979396167291.07767252391-0.3058066240580.8116911570540.0354076031132-0.2588745519090.2751101700970.1238902749810.0928526258779-0.283359009697-0.968557403063-0.1042540570360.03576601111511.27828564247-0.2626772008930.07299016810750.00525300547013-0.1894800167110.721181230371102.743815028101.745365127287.314595663
31.045741220640.329176068063-0.2529371829592.05576258840.8358513024011.0975314068-0.109532061782-0.3208431687530.3041880456770.1017022024030.2767719427480.41991240575-0.734134245654-0.8478166309670.09462501238911.18782388450.428914909270.01182566039570.727860113831-0.04041737731570.43891379033269.4271402426108.587436806283.513212539
41.0212020767-0.943694095616-0.5046058474092.206798351640.552773612072.292243600410.11677038228-0.114082414984-0.1713458032470.358847443386-0.1126161320050.0659372873241-0.4819258665960.0532573589115-0.02810834658220.682260017493-0.276218696202-0.05224094829490.5194993999810.06225357591510.43925344673997.919131075877.4568664531328.698267003
51.326696491520.1510722672110.146470241461.011603327580.3377894603181.6606617440.147926226710.05342558513360.1627404998420.177998914435-0.24310106025-0.0916958246417-0.9560040019540.03087579422240.1349938107531.51703111881-0.2481342464320.1239413027040.548305975237-0.03295466122750.526271351997101.287154053104.387960839343.603297437
61.46327251379-0.693480281462-0.2505710951431.874340981940.8217582673174.123056238710.269365181939-0.2422863013-0.1301977166210.674254959442-0.184392295041-0.268545402723-0.1347421263170.28005941794-0.08112473593040.84001281319-0.392255559785-0.1248668436060.5707945349810.06432539054980.477891044827108.03218981470.3856726772349.027183802
70.762667956515-0.6046238911670.5577520495811.51855461401-0.704798187792.70619107441-0.0146057275618-0.1159602327250.02456090005690.1798363607750.06425631942820.163592385845-0.31412331141-0.196843752971-0.03137995159630.2896838801570.02949152560660.1281411626130.357980968426-0.03115253327350.457368325595144.829245181165.296879407211.047238589
80.346291630299-0.221508290181-0.6641780668440.391415581150.1069803109282.398640773270.07547046849910.0542721548771-0.22842589440.2019420676590.0394861188839-0.02330959684550.473790461745-0.48333860448-0.09528621667420.591161233667-0.1282896937920.01073509567590.2853814987970.07360041611580.654793275383141.275579319139.928726041226.68021512
92.7071814895-0.7391619316010.829198528562.22560708146-0.2698598981133.89304650562-0.0229939482399-0.132753155611-0.1019922961980.3417585320050.1291143673630.391287270395-0.592232801645-0.854716107371-0.08751622519030.5500431210550.1028137759360.1719467374430.2643611194860.004457830514530.470853833787133.264897573173.213913651228.962136215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 266 )
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 728 )
3X-RAY DIFFRACTION3chain 'A' and (resid 729 through 967 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 266 )
5X-RAY DIFFRACTION5chain 'B' and (resid 267 through 706 )
6X-RAY DIFFRACTION6chain 'B' and (resid 707 through 967 )
7X-RAY DIFFRACTION7chain 'C' and (resid 5 through 266 )
8X-RAY DIFFRACTION8chain 'C' and (resid 267 through 728 )
9X-RAY DIFFRACTION9chain 'C' and (resid 729 through 967 )

+
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://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