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- PDB-1svd: The structure of Halothiobacillus neapolitanus RuBisCo -

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Basic information

Entry
Database: PDB / ID: 1svd
TitleThe structure of Halothiobacillus neapolitanus RuBisCo
Components
  • Ribulose bisphosphate carboxylase small chain
  • ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
KeywordsLYASE / beta-alpha-barrel
Function / homology
Function and homology information


carboxysome / 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, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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 / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-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 bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsKerfeld, C.A. / Sawaya, M.R. / Pashkov, I. / Cannon, G. / Williams, E. / Tran, K. / Yeates, T.O.
CitationJournal: To be Published
Title: The structure of Halothiobacillus neapolitanus RuBisCo
Authors: Kerfeld, C.A. / Sawaya, M.R. / Pashkov, I. / Cannon, G. / Williams, E. / Tran, K. / Yeates, T.O.
History
DepositionMar 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
M: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8535
Polymers65,5692
Non-polymers2843
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-38 kcal/mol
Surface area23050 Å2
MethodPISA
2
A: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
M: Ribulose bisphosphate carboxylase small chain
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)526,82640
Polymers524,55316
Non-polymers2,27424
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area84410 Å2
ΔGint-520 kcal/mol
Surface area129540 Å2
MethodPISA
3
A: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
M: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
M: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,70710
Polymers131,1384
Non-polymers5686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14300 Å2
ΔGint-109 kcal/mol
Surface area39190 Å2
MethodPISA
4
A: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
M: Ribulose bisphosphate carboxylase small chain
hetero molecules

A: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit
M: Ribulose bisphosphate carboxylase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,70710
Polymers131,1384
Non-polymers5686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area9380 Å2
ΔGint-93 kcal/mol
Surface area44100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.066, 157.066, 107.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

21M-170-

HOH

DetailsThe biological assembly is an L(8)S(8) octamer generated from the large(L) and small (S) subnits in the asymmetric unit by the operations: X,Y,Z; -X,-Y,Z; -Y,X,Z; Y,-X,Z; -X,Y,-Z; X,-Y,-Z; Y,X,-Z; -Y,-X,-Z.

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Components

#1: Protein ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit


Mass: 52702.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halothiobacillus neapolitanus (bacteria)
References: UniProt: O85040, ribulose-bisphosphate carboxylase
#2: Protein Ribulose bisphosphate carboxylase small chain / RuBisCO small subunit


Mass: 12866.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halothiobacillus neapolitanus (bacteria)
References: UniProt: P45686, ribulose-bisphosphate carboxylase
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: ammonium sulfate, citrate, cobalt chloride, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2003 / Details: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. all: 62138 / Num. obs: 62138 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rsym value: 0.091 / Net I/σ(I): 19.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 8.7 / Rsym value: 0.355 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR
Starting model: pdb entry 1rbl

1rbl


Resolution: 1.8→87.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.538 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16574 3095 5 %RANDOM
Rwork0.14502 ---
obs0.14608 58984 99.95 %-
all-58984 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.186 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 16 354 4739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214544
X-RAY DIFFRACTIONr_bond_other_d0.0020.024008
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9356169
X-RAY DIFFRACTIONr_angle_other_deg0.9139305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8935559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025150
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02984
X-RAY DIFFRACTIONr_nbd_refined0.2090.2881
X-RAY DIFFRACTIONr_nbd_other0.2460.24649
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2302
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.2137
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.52764
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75924432
X-RAY DIFFRACTIONr_scbond_it2.66531780
X-RAY DIFFRACTIONr_scangle_it4.2074.51737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.198 237
Rwork0.162 4304
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0958-0.08460.05870.2307-0.1110.2864-0.0113-0.00120.04850.0068-0.008-0.0588-0.02510.03710.01920.0268-0.01790.00120.0381-0.00790.059319.654330.168612.6002
20.48160.16170.23050.31820.16290.17550.0296-0.10760.05320.0481-0.0370.0341-0.0184-0.04680.00730.0550.0010.00990.0606-0.02170.01313.611929.692141.0339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 46016 - 460
2X-RAY DIFFRACTION2MB3 - 1103 - 110

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