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- PDB-1bwv: Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bwv | ||||||
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Title | Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate | ||||||
![]() | (PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)) x 2 | ||||||
![]() | LYASE / CARBON DIOXIDE FIXATION / COMPLEX (RUBISCO-REACTION INTERMEDIATE) / HIGH SPECIFICITY FACTOR | ||||||
Function / homology | ![]() ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugawara, H. / Yamamoto, H. / Shibata, N. / Inoue, T. / Miyake, C. / Yokota, A. / Kai, Y. | ||||||
![]() | ![]() Title: Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita. Authors: Sugawara, H. / Yamamoto, H. / Shibata, N. / Inoue, T. / Okada, S. / Miyake, C. / Yokota, A. / Kai, Y. #1: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 493.8 KB | Display | ![]() |
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PDB format | ![]() | 402.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 87.9 KB | Display | |
Data in CIF | ![]() | 121.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rblS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE ENZYME IS HEXADECAMER AND CONSISTS OF EIGHT LARGE AND EIGHT SMALL SUBUNITS. THE CHAINS ID'S OF LARGE SUBUNITS ARE A,B,C,D,E,F,G AND H. THE CHAINS ID'S OF SMALL SUBUNITS ARE S,T,U,V,W,X,Y AND Z. FOUR LARGE SUBUNITS (L) AND FOUR SMALL SUBUNITS (S) ARE CONTAINED IN THE ASYMMETRIC UNIT. A PAIR OF L4S4 UNITS RELATED BY THE CRYSTALLOGRAPHIC 2-FOLD GENERATES THE HEXADECAMER. CATALYTIC UNITS OF THE ENZYME AR L2S2 WHICH IS CONSTITUTED BY CHAINS ABST, CDUV, EFWX AND GHY OF THE HEXADECAMER. |
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Components
#1: Protein | Mass: 55101.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: THE ENZYME IS COMPLEXED WITH CARBON DIOXIDE, MG2+ AND REACTION INTERMEDIATE ANALOGUE, 2-CARBOXYARABINITOL 1,5-BISPHOSPHATE. RESIDUE 201, KCX, OF THE LARGE SUBUNIT IS A LYS CARBAMYLATED AT THE EPSILON-AMINO GROUP Source: (natural) ![]() References: UniProt: O98949, ribulose-bisphosphate carboxylase #2: Protein | Mass: 16179.422 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: THE ENZYME IS COMPLEXED WITH CARBON DIOXIDE, MG2+ AND REACTION INTERMEDIATE ANALOGUE, 2-CARBOXYARABINITOL 1,5-BISPHOSPHATE. RESIDUE 201, KXC, OF THE LARGE SUBUNIT IS A LYS CARBAMYLATED AT THE EPSILON-AMINO GROUP Source: (natural) ![]() References: UniProt: O98950, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-MG / #4: Sugar | ChemComp-CAP / #5: Water | ChemComp-HOH / | Nonpolymer details | KCX: THE EPSILON AMINO GROUP OF LYSINE 201 IS CARBAMYLAT | Sequence details | THE RESIDUE NUMBERING OF SPINACH RUBISCO HAS BEEN USED IN GALDIERIA ENZYME. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 9% PEG8000, 4% MPD, 50 MM HEPES PH7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Mar 15, 1998 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 277331 / % possible obs: 86.4 % / Observed criterion σ(I): 0.5 / Redundancy: 3.2 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.203 / % possible all: 58.1 |
Reflection | *PLUS Num. obs: 83303 / Num. measured all: 277331 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RBL Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARAM19X.PRO / Topol file: TPPH19X.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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