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- PDB-1rcx: NON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBUL... -

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Basic information

Entry
Database: PDB / ID: 1rcx
TitleNON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE
Components(RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2
KeywordsLYASE (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 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, 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
RIBULOSE-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH PDB ENTRY 1RCO / Resolution: 2.4 Å
AuthorsTaylor, T.C. / Andersson, I.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate.
Authors: Taylor, T.C. / Andersson, I.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Large Structures at High Resolution: The 1.6 A Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Complexed with 2-Carboxyarabinitol Bisphosphate
Authors: Andersson, I.
History
DepositionDec 6, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
L: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
S: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
B: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
C: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
E: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
F: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
H: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
I: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
K: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
M: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
O: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
P: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
R: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
T: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
V: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
W: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)541,46824
Polymers538,98716
Non-polymers2,4818
Water31,8511768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110020 Å2
ΔGint-475 kcal/mol
Surface area116240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.300, 219.000, 113.500
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(0.96562, 0.21886, 0.140279), (0.218875, -0.97563, 0.015511), (0.140255, 0.015726, -0.989991)-15.9421, 104.2701, 60.6314
2given(0.002938, -0.993493, -0.113853), (0.999828, 0.000836, 0.018505), (-0.018289, -0.113888, 0.993325)-0.052, 97.2979, 4.6987
3given(-0.229902, 0.968377, 0.096907), (0.968338, 0.217659, 0.122252), (0.097293, 0.121945, -0.987757)-110.5011, 82.5915, 53.3554
4given(-0.991742, 0.008038, -0.127996), (0.004456, -0.995271, -0.097031), (-0.128171, -0.0968, 0.987017)-97.2089, 97.4964, -1.4776
5given(-0.974164, -0.22562, -0.009962), (-0.225691, 0.970978, 0.079157), (-0.008186, 0.079361, -0.996812)-88.4937, -12.0878, 50.2928
6given(0.005318, 0.999912, -0.012176), (-0.993416, 0.003889, -0.114498), (-0.11444, 0.012705, 0.993349)-97.0873, 0.3601, -6.1495
7given(0.223928, -0.973976, 0.035028), (-0.974117, -0.224809, -0.023603), (0.030863, -0.028836, -0.999108)6.2151, 9.7116, 57.5037
DetailsTHE DEPOSITORS PROVIDED CHAINS L AND S. THE OTHER CHAINS TO MAKE THE COMPLETE ASYMMETRIC UNIT WERE GENERATED BY THE PROTEIN DATA BANK USING THE MTRIX TRANSFORMATIONS BELOW.

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Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE / RUBISCO


Mass: 52734.680 Da / Num. of mol.: 8 / 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/OXYGENASE / RUBISCO


Mass: 14638.671 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF
References: UniProt: P00870, ribulose-bisphosphate carboxylase
#3: Sugar
ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1768 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.8
Details: 12% PEG 4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 20 MM RUBP
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
220 mMRuBP1drop
311-13 %(w/v)PEG40001reservoir
40.2 M1reservoirNaCl
525 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 149428 / % possible obs: 70.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.8 / % possible all: 65
Reflection
*PLUS
Num. measured all: 959052 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1RCO
Resolution: 2.4→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 6443 5 %RANDOM
Rwork0.224 ---
obs0.224 143806 63 %-
Refinement stepCycle: LAST / Resolution: 2.4→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 18 221 4921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.937
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.53
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.4→2.5 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.316 536 5 %
Rwork0.289 16384 -
obs--67.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARAWAT.TOP
X-RAY DIFFRACTION3RUBP.PARARUBP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.53

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