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- PDB-1aa1: ACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGL... -

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Basic information

Entry
Database: PDB / ID: 1aa1
TitleACTIVATED SPINACH RUBISCO IN COMPLEX WITH THE PRODUCT 3-PHOSPHOGLYCERATE
Components
  • RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
  • RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
KeywordsOXIDOREDUCTASE / LYASE (CARBON-CARBON)
Function / homologyRibulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase small chain, domain / RuBisCO / Ribulose bisphosphate carboxylase, small chain / Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase, large subunit, C-terminal / Ribulose bisphosphate carboxylase, small subunit superfamily ...Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase small chain, domain / RuBisCO / Ribulose bisphosphate carboxylase, small chain / Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase, large subunit, C-terminal / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / photorespiration / carbon fixation / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / photosynthesis / chloroplast / monooxygenase activity / magnesium ion binding / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small chain 2, chloroplastic
Function and homology information
Specimen sourceSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.2 Å resolution
AuthorsTaylor, T.C. / Andersson, I.
Citation
Journal: Biochemistry / Year: 1997
Title: Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 20, 1997 / Release: Jul 7, 1997
RevisionDateData content typeGroupProviderType
1.0Jul 7, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
S: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,25120
Polyers269,6658
Non-polymers1,58612
Water18,1591008
1
L: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
S: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
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)
hetero molecules

L: RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN)
S: RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN)
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,50240
Polyers539,33116
Non-polymers3,17124
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area (Å2)102510
ΔGint (kcal/M)-473
Surface area (Å2)116560
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)157.600, 158.700, 203.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: Protein/peptide
RIBULOSE BISPHOSPHATE CARBOXYLASE (LARGE CHAIN) / RUBISCO


Mass: 52777.680 Da / Num. of mol.: 4 / Source: (natural) Spinacia oleracea (spinach) / Genus: Spinacia / Organ: LEAF
References: UniProt: P00875, ribulose-bisphosphate carboxylase
#2: Protein/peptide
RIBULOSE BISPHOSPHATE CARBOXYLASE (SMALL CHAIN) / RUBISCO


Mass: 14638.671 Da / Num. of mol.: 4 / Source: (natural) Spinacia oleracea (spinach) / Genus: Spinacia / Organ: LEAF
References: UniProt: Q43832, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#4: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 8 / Formula: C3H7O7P / 3-Phosphoglyceric acid
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1008 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 2.36 / Density percent sol: 4 %
Crystal growpH: 7.2
Details: 14% PEG 4000, 0.2 M NACL, 25 MM HEPES PH 7.8 10 MM MGCL2, 100 MM 3-PHOSPHOGLYCERATE, pH 7.2
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Taylor, T.C., (1996) Nat. Struct. Biol., 3, 95.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
150-60 mg/mlprotein1drop
2100 mM3-PGA1drop
314-16 %PEG40001reservoir
40.2 M1reservoirNaCl
525 mMHEPES1reservoir
610 mM1reservoirMgCl2
750 mM1reservoirNaHCO3
80.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 283 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.5 / Synchrotron site: SRS / Beamline: PX9.5 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Oct 1, 1994
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionD resolution high: 2.2 Å / D resolution low: 2 Å / Number obs: 107965 / Rmerge I obs: 0.103 / NetI over sigmaI: 9.8 / Redundancy: 7.4 % / Percent possible obs: 85
Reflection shellRmerge I obs: 0.205 / Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / MeanI over sigI obs: 4.7 / Percent possible all: 75
Reflection
*PLUS
Number measured all: 799161

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefineR Free selection details: RANDOM / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / Sigma F: 0
Least-squares processR factor R free: 0.224 / R factor R work: 0.207 / R factor obs: 0.207 / Highest resolution: 2.2 Å / Lowest resolution: 7 Å / Number reflection R free: 3261 / Number reflection obs: 104308 / Percent reflection R free: 3 / Percent reflection obs: 83.8
Refine hist #LASTHighest resolution: 2.2 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 17856 / Nucleic acid: 0 / Ligand: 92 / Solvent: 1008 / Total: 18956
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.667
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.256
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
Refine LS shellHighest resolution: 2.2 Å / R factor R free: 0.252 / R factor R work: 0.261 / Lowest resolution: 2.3 Å / Number reflection R free: 293 / Number reflection R work: 10188 / Total number of bins used: 8 / Percent reflection R free: 3 / Percent reflection obs: 67.7
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARAWAT.TOP
X-RAY DIFFRACTION3PGA.PARAPGA.TOP
X-RAY DIFFRACTION4CARB.PARACARB.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_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.256

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