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- PDB-1bwv: Activated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISC... -

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Basic information

Entry
Database: PDB / ID: 1bwv
TitleActivated Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) Complexed with the Reaction Intermediate Analogue 2-Carboxyarabinitol 1,5-Bisphosphate
Components(PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)) x 2
KeywordsLYASE / CARBON DIOXIDE FIXATION / COMPLEX (RUBISCO-REACTION INTERMEDIATE) / HIGH SPECIFICITY FACTOR
Function / homology
Function and homology information


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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Multifunctional fusion protein
Similarity search - Component
Biological speciesGaldieria partita (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSugawara, H. / Yamamoto, H. / Shibata, N. / Inoue, T. / Miyake, C. / Yokota, A. / Kai, Y.
Citation
Journal: J.Biol.Chem. / Year: 1999
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: 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
DepositionSep 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 27, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
S: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
U: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
W: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
Y: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,64616
Polymers285,1258
Non-polymers1,5228
Water9,764542
1
A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
S: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
U: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
W: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
Y: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
hetero molecules

A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
S: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
U: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
W: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
Y: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)573,29332
Polymers570,24916
Non-polymers3,04316
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area108770 Å2
ΔGint-458 kcal/mol
Surface area124270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.070, 117.070, 319.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.500118, 0.865957, 1.4E-5), (0.865957, 0.500118, 8.0E-6), (1.6E-5, -1)0.0007, -0.0048, -34.6259
2given(0.251408, 0.432654, -0.865797), (0.43198, 0.750334, 0.500392), (0.866134, -0.499809, 0.001742)-15.0259, 8.7038, -17.2249
3given(-0.500062, 0.86599, -4.0E-6), (0.86599, 0.500062, 9.2E-5), (8.1E-5, 4.2E-5, -1)-0.0034, 0.0013, -34.6265
4given(0.248883, 0.434033, 0.865836), (0.433806, 0.749325, -0.500325), (-0.86595, 0.500127, -0.001792)14.9533, -8.6235, -17.2889
5given(-0.500229, 0.865893, 0.000498), (0.865893, 0.500228, -0.000548), (-0.000225, -0.000706, -1)-0.0048, -0.0252, -34.5896
6given(0.251848, 0.433964, -0.865014), (0.43325, 0.748694, 0.501748), (0.865371, -0.501131, 0.000542)-15.0279, 8.734, -17.23
7given(-0.500199, 0.86591, 7.2E-5), (0.86591, 0.500199, -7.0E-5), (-9.6E-5, 2.7E-5, -1)-0.0005, 0.004, -34.6219
8given(0.249883, 0.435122, 0.865001), (0.431542, 0.749666, -0.501769), (-0.866793, 0.498668, -0.000445)14.922, -8.6347, -17.2512
DetailsTHE 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
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE) / E.C.4.1.1.39 LYASE / RUBISCO


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) Galdieria partita (eukaryote) / Organelle: CHLOROPLAST
References: UniProt: O98949, ribulose-bisphosphate carboxylase
#2: Protein
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE) / E.C.4.1.1.39 LYASE / RUBISCO


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) Galdieria partita (eukaryote) / Organelle: CHLOROPLAST
References: UniProt: O98950, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#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.: 542 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsKCX: THE EPSILON AMINO GROUP OF LYSINE 201 IS CARBAMYLATED.
Sequence detailsTHE RESIDUE NUMBERING OF SPINACH RUBISCO HAS BEEN USED IN GALDIERIA ENZYME.

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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: 2.55 Å3/Da / Density % sol: 51.5 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
110.0 Mprotein1drop
220 mM1dropMgCl2
320 mM1dropNaHCO3
42 mM2-CABP1drop
550 mMHEPES1reservoir
69 %PEG80001reservoir
74 %MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 15, 1998
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
AMoREphasing
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RBL

1rbl


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4149 5 %RANDOM
Rwork0.163 ---
obs0.163 82988 86 %-
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19408 0 88 542 20038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TPPH19X.PRO
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.55

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