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- PDB-1bxn: THE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS TO 2.... -

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Basic information

Entry
Database: PDB / ID: 1bxn
TitleTHE CRYSTAL STRUCTURE OF RUBISCO FROM ALCALIGENES EUTROPHUS TO 2.7 ANGSTROMS.
Components
  • PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
  • PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
KeywordsLYASE / LYASE (CARBON-CARBON)
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / 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 / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, small subunit / 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
PHOSPHATE ION / Ribulose bisphosphate carboxylase small subunit, chromosomal / Ribulose bisphosphate carboxylase large chain, chromosomal
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHansen, S. / Vollan, V.B. / Hough, E. / Andersen, K.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits.
Authors: Hansen, S. / Vollan, V.B. / Hough, E. / Andersen, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification, Crystallization and Preliminary X-Ray Studies of Two Isoforms of Rubisco from Alcaligenes Eutrophus
Authors: Hansen, S. / Hough, E. / Andersen, K.
History
DepositionOct 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
I: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
J: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
K: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
L: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,81116
Polymers279,0518
Non-polymers7608
Water00
1
A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
I: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
J: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
K: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
L: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
hetero molecules

A: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
I: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
C: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
J: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
E: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
K: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
G: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)
L: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)559,62232
Polymers558,10316
Non-polymers1,52016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area95060 Å2
ΔGint-442 kcal/mol
Surface area121570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.000, 112.000, 402.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.013, -0.987, 0.163), (1, 0.014, 0.001), (-0.003, 0.163, 0.987)93.962, 100.378, -16.079
2given(0.014, -0.986, 0.168), (1, 0.014, -0.001), (-0.001, 0.168, 0.986)93.52, 100.51, -16.493
3given(-0.987, 0.006, 0.16), (0.02, -0.987, 0.162), (0.159, 0.164, 0.974)-6.824, 196.01401, -15.705
4given(-0.986, 0.012, 0.165), (0.015, -0.987, 0.162), (0.165, 0.162, 0.973)-7.689, 196.035, -15.434
5given(0.004, 1), (-0.987, 0.004, 0.161), (0.161, -0.001, 0.987)-101.89, 95.244, 0.533
6given(0.008, 1, 0.002), (-0.986, 0.008, 0.166), (0.166, -0.004, 0.986)-102.032, 94.507, 0.958

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Components

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


Mass: 53703.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria)
References: UniProt: P0C2C2*PLUS, ribulose-bisphosphate carboxylase
#2: Protein
PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN) / RUBISCO


Mass: 16058.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria)
References: UniProt: P09658*PLUS, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4

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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: 2.44 Å3/Da / Density % sol: 45.8 %
Crystal growpH: 8.4 / Details: pH 8.40
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
220 mMHEPES1drop
30.7-0.8 M1reservoirK2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.9117
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 1997
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 65785 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 1.5
Reflection
*PLUS
% possible obs: 87.5 %
Reflection shell
*PLUS
Highest resolution: 2.65 Å / Lowest resolution: 2.79 Å / % possible obs: 89.1 % / Redundancy: 4.3 % / Num. unique obs: 9546 / Rmerge(I) obs: 0.695

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUS

1aus


Resolution: 2.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.322 -10 %RANDOM
Rwork0.266 ---
obs0.266 65785 90 %-
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18104 0 40 0 18144
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
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
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.76
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11

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