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- PDB-1upm: ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BI... -

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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 / 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: 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
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
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

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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.: 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: saccharide / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2
#5: Water ChemComp-HOH / 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.
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: 2.6 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

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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

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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

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