[English] 日本語
Yorodumi
- PDB-1upm: ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1upm
TitleACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.
Components
  • RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
  • RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
KeywordsLYASE / CARBON-CARBON / OXIDOREDUCTASE / PHOTOSYNTHESIS / CARBON-DIOXIDE FIXATION LYASE (CARBON-CARBON)
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsKarkehabadi, S. / Taylor, T.C. / Andersson, I.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Calcium Supports Loop Closure But not Catalysis in Rubisco
Authors: Karkehabadi, S. / Taylor, T.C. / Andersson, I.
History
DepositionOct 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
F: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
H: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
K: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
L: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
M: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
O: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
P: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
R: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
S: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
T: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
V: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
W: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,07732
Polymers539,90716
Non-polymers3,17016
Water50,2262788
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)219.600, 220.942, 116.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.9754, 0.1631, 0.1485), (0.1631, -0.9865, 0.01194), (0.1484, 0.01258, -0.9888)-13.16, 102.7, 62.17
3given(0.004226, 0.9999, -0.0157), (-0.9924, 0.002264, -0.1229), (-0.1229, 0.0161, 0.9923)-97.89, 0.5825, -6.762
4given(-0.1757, 0.9781, 0.1118), (0.9783, 0.1609, 0.1304), (0.1095, 0.1322, -0.9851)-109.5, 86.07, 54.33
5given(-0.991, 0.006136, -0.134), (0.008826, -0.9938, -0.1108), (-0.1338, -0.111, 0.9848)-97.71, 98.66, -1.161
6given(-0.9852, -0.1716, -0.003444), (-0.1711, 0.9803, 0.09862), (-0.01355, 0.09774, -0.9951)-92.57, -10.56, 50.11
7given(0.006028, -0.9916, -0.129), (0.9999, 0.004664, 0.01088), (-0.01018, -0.1291, 0.9916)0.4245, 97.93, 5.867
8given(0.1676, -0.9856, 0.02393), (-0.9856, -0.1681, -0.02077), (0.02449, -0.0201, -0.9995)4.103, 6.252, 57.76
9given(1), (1), (1)
10given(0.9741, 0.1732, 0.1453), (0.1722, -0.9849, 0.01982), (0.1466, 0.005719, -0.9892)-13.53, 103, 62.35
11given(0.01118, 0.9998, -0.01337), (-0.9917, 0.009374, -0.1283), (-0.1282, 0.01469, 0.9916)-97.55, 0.4683, -6.964
12given(-0.181, 0.9774, 0.1095), (0.9768, 0.1657, 0.1358), (0.1146, 0.1315, -0.9847)-109.7, 85.63, 54.59
13given(-0.9912, 0.007847, -0.1322), (0.007278, -0.9935, -0.1135), (-0.1322, -0.1135, 0.9847)-97.83, 98.65, -0.9236
14given(-0.9832, -0.1823, -0.00858), (-0.1822, 0.9775, 0.1063), (-0.01099, 0.1061, -0.9943)-91.68, -11.13, 49.72
15given(-0.002603, -0.992, -0.126), (1, -0.00315, 0.004136), (-0.0045, -0.126, 0.992)0.00952, 98.62, 5.938
16given(0.1697, -0.9852, 0.02303), (-0.9852, -0.1701, -0.0198), (0.02343, -0.01933, -0.9995)4.253, 6.396, 57.64

-
Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE / RUBISCO LARGE SUBUNIT


Mass: 52849.742 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / Tissue: LEAF
References: UniProt: P00875, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN / RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE / RUBISCO SMALL SUBUNIT


Mass: 14638.671 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: THE COMPLETE STRUCTURE HAS BEEN SUBMITTED AS WELL AS THE MATRIX TRANSFORMATION FOR EACH CHAIN.
Source: (natural) SPINACIA OLERACEA (spinach) / Organ: LEAF
References: UniProt: Q43832, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2788 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRUBISCO CATALYZES THE CARBOXYLATION OF D-RIBULOSE 1,5- BISPHOSPHATE AS WELL AS THE OXIDATIVE ...RUBISCO CATALYZES THE CARBOXYLATION OF D-RIBULOSE 1,5- BISPHOSPHATE AS WELL AS THE OXIDATIVE FRAGMENTATION OF PENTOSE SUBSTRATE IN PHOTORESPIRATION. THE PROTEIN IS A COMPLEX OF 8 LARGE AND 8 SMALL CHAINS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.8
Details: 10% PEG 4000, 0.1 M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 1MM 2-CABP
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1dropNaHCO3
210 mM1dropCaCl2
30.1 MHEPES1droppH7.8
460 mg/mlprotein1drop
5100 mM3PGA1drop
60.1 MHEPES1reservoirpH7.8
70.1 M1reservoirNaHCO3
810 mM1reservoirCaCl2
90.1-0.2 M1reservoirNaCl
1010-14 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9386
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9386 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 226289 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.1 / % possible all: 70.6
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 90.2 % / Num. measured all: 2722153 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 70.6 % / Rmerge(I) obs: 0.15

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.3→20 Å / SU B: 5.994 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.364 / ESU R Free: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2 11379 5 %RANDOM
Rwork0.23 ---
obs-251201 90 %-
Displacement parametersBiso mean: 32.408 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2---0.39 Å20 Å2
3---2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37472 0 176 2788 40436
Refinement
*PLUS
Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.7

+
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