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- PDB-1upp: SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT... -

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Basic information

Entry
Database: PDB / ID: 1upp
TitleSPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium.
Components
  • RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
  • RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
KeywordsLYASE / CARBON-CARBON / OXIDOREDUCTASE / PHOTOSYNTHESIS / CARBON-DIOXIDE FIXATION
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 / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-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 / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-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: Karehabadi, S. / Taylor, T.C. / Andersson, I.
History
DepositionOct 9, 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
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
J: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
K: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
L: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,53816
Polymers269,9548
Non-polymers1,5858
Water11,962664
1
A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
J: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
K: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
L: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
hetero molecules

A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
I: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
J: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
K: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
L: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)543,07732
Polymers539,90716
Non-polymers3,17016
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)155.880, 156.250, 199.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.002971, -0.9996, -0.02932), (0.9995, 0.002027, 0.03217), (-0.0321, -0.0294, 0.9991)40.8, 37.5, 1.187
2given(-0.9982, -0.000725, -0.0599), (0.000669, -1, 0.000961), (-0.0599, 0.000919, 0.9982)3.037, 78.37, 0.01699
3given(-0.00076, 0.9996, -0.02909), (-0.9996, -0.001593, -0.02862), (-0.02865, 0.02906, 0.9992)-37.6, 40.69, -1.152
4given(0.004315, -0.9996, -0.02929), (0.9996, 0.003458, 0.02926), (-0.02915, -0.02941, 0.9991)40.76, 37.58, 1.142
5given(-0.9981, -0.000958, -0.0618), (0.001024, -1, -0.00103), (-0.0618, -0.001092, 0.9981)3.032, 78.38, 0.1063
6given(-0.001617, 0.9993, -0.03642), (-0.9996, -0.002643, -0.02813), (-0.02821, 0.03636, 0.9989)-37.59, 40.75, -1.301

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Components

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


Mass: 52849.742 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / Organ: 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.: 4 / Source method: isolated from a natural source
Details: THIS IS THE SECOND STRUCTURE OF THIS COMPLEX THAT IS BEING SUBMITTED. THE PREVOUS STRUCTURE, PDB ID CODE 1UPM, WAS OBTAINED FROM A CRYSTAL OF RUBISCO-CA COOCRYSTALLIZED WITH 2-CABP WHERAS ...Details: THIS IS THE SECOND STRUCTURE OF THIS COMPLEX THAT IS BEING SUBMITTED. THE PREVOUS STRUCTURE, PDB ID CODE 1UPM, WAS OBTAINED FROM A CRYSTAL OF RUBISCO-CA COOCRYSTALLIZED WITH 2-CABP WHERAS THIS STRUCTURE IS FROM A RUBISCO-CA/3PGA CRYSTAL WHICH WAS SOAKED WITH 2-CABP
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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O13P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / 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.
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.8
Details: 10% PEG 4000, 0.1M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 0.1 M 3PGA THEN SOAKED IN 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

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / 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→100 Å / Num. obs: 108187 / % possible obs: 76.1 % / Observed criterion σ(I): 2 / Redundancy: 17.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.12 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.1 / % possible all: 70
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 108187 / % possible obs: 76.1 % / Num. measured all: 1884294 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 70 % / Rmerge(I) obs: 0.24

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.3→100 Å / SU B: 9.449 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.539 / ESU R Free: 0.314 / Details: THE DATA IS FROM A MEROHEDRALLY TWINNED CRYSTAL
RfactorNum. reflection% reflectionSelection details
Rfree0.3071 5500 5.1 %RANDOM
Rwork0.25598 ---
obs0.25862 102132 76.1 %-
Displacement parametersBiso mean: 25.364 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18752 0 88 664 19504
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.016
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.7

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