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- PDB-4lf2: Hexameric Form II RuBisCO from Rhodopseudomonas palustris, activa... -

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Basic information

Entry
Database: PDB / ID: 4lf2
TitleHexameric Form II RuBisCO from Rhodopseudomonas palustris, activated and complexed with sulfate and magnesium
ComponentsRibulose bisphosphate carboxylase
Keywordslyase / oxidoreductase / Form II / CbbM 2-CABP / Transition-State Analog / Reaction Intermediate Analogue / photosynthesis / photosynthetic carbon fixation
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 large subunit, type II / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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 ...Ribulose bisphosphate carboxylase large subunit, type II / RuBisCO large subunit, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / 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
CARBONATE ION / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsChan, S. / Satagopan, S. / Sawaya, M.R. / Eisenberg, D. / Tabita, F.R. / Perry, L.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure-function studies with the unique hexameric form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Rhodopseudomonas palustris.
Authors: Satagopan, S. / Chan, S. / Perry, L.J. / Tabita, F.R.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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 bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,97425
Polymers316,5446
Non-polymers1,43019
Water24,5361362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36740 Å2
ΔGint-416 kcal/mol
Surface area79850 Å2
MethodPISA
2
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,06810
Polymers105,5152
Non-polymers5538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-143 kcal/mol
Surface area28930 Å2
MethodPISA
3
C: Ribulose bisphosphate carboxylase
D: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0089
Polymers105,5152
Non-polymers4937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-145 kcal/mol
Surface area29150 Å2
MethodPISA
4
E: Ribulose bisphosphate carboxylase
F: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8996
Polymers105,5152
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-121 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.221, 99.777, 100.000
Angle α, β, γ (deg.)67.300, 71.280, 86.630
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTRPTRPAA1 - 45221 - 472
21METMETTRPTRPBB1 - 45221 - 472
12METMETTRPTRPAA1 - 45221 - 472
22METMETTRPTRPCC1 - 45221 - 472
13METMETLYSLYSAA1 - 45721 - 477
23METMETLYSLYSDD1 - 45721 - 477
14ASPASPLYSLYSAA2 - 45522 - 475
24ASPASPLYSLYSEE2 - 45522 - 475
15ASPASPLEULEUAA2 - 45622 - 476
25ASPASPLEULEUFF2 - 45622 - 476
16METMETARGARGBB1 - 45321 - 473
26METMETARGARGCC1 - 45321 - 473
17METMETTRPTRPBB1 - 45221 - 472
27METMETTRPTRPDD1 - 45221 - 472
18ASPASPTRPTRPBB2 - 45222 - 472
28ASPASPTRPTRPEE2 - 45222 - 472
19ASPASPTRPTRPBB2 - 45222 - 472
29ASPASPTRPTRPFF2 - 45222 - 472
110METMETTRPTRPCC1 - 45221 - 472
210METMETTRPTRPDD1 - 45221 - 472
111ASPASPTRPTRPCC2 - 45222 - 472
211ASPASPTRPTRPEE2 - 45222 - 472
112ASPASPTRPTRPCC2 - 45222 - 472
212ASPASPTRPTRPFF2 - 45222 - 472
113ASPASPLYSLYSDD2 - 45522 - 475
213ASPASPLYSLYSEE2 - 45522 - 475
114ASPASPLEULEUDD2 - 45622 - 476
214ASPASPLEULEUFF2 - 45622 - 476
115ASPASPLYSLYSEE2 - 45522 - 475
215ASPASPLYSLYSFF2 - 45522 - 475

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO


Mass: 52757.340 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: cbbM, RPA4641, Rpal_5122 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q6N0W9, ribulose-bisphosphate carboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1362 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 170 mM lithium sulfate, 85 mM Tris-HCl, 24 % PEG 4000, 14 % glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→90 Å / Num. obs: 184523 / % possible obs: 85.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.139 / Χ2: 1.143 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.10.75484411.647139.1
1.92-1.993.10.558121031.31156
1.99-2.0830.411177661.314182.2
2.08-2.193.30.337202561.183193.7
2.19-2.333.60.284207791.205196.1
2.33-2.513.60.207209201.108196.9
2.51-2.763.70.168210071.077197.3
2.76-3.163.70.132210531.05197.5
3.16-3.993.70.111211381.031197.8
3.99-903.70.11210601.014197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å87.29 Å
Translation2.5 Å87.29 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→87.43 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2882 / WRfactor Rwork: 0.2282 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8153 / SU B: 8.347 / SU ML: 0.202 / SU R Cruickshank DPI: 1.7826 / SU Rfree: 0.3124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.783 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 4852 5 %RANDOM
Rwork0.2026 ---
obs0.2053 96925 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 188.66 Å2 / Biso mean: 24.4126 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0.22 Å2-1.15 Å2
2---0.56 Å20.25 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.38→87.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21129 0 76 1362 22567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01921744
X-RAY DIFFRACTIONr_bond_other_d0.0050.0220071
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.94329449
X-RAY DIFFRACTIONr_angle_other_deg1.451346054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.54652745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63223.6841045
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.209153352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8615138
X-RAY DIFFRACTIONr_chiral_restr0.0830.23075
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02125323
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025363
X-RAY DIFFRACTIONr_mcbond_it8.9012.92310938
X-RAY DIFFRACTIONr_mcbond_other8.8852.92210937
X-RAY DIFFRACTIONr_mcangle_it10.6684.8913667
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A275010.07
12B275010.07
21A274320.06
22C274320.06
31A278430.06
32D278430.06
41A276310.05
42E276310.05
51A276420.06
52F276420.06
61B275580.06
62C275580.06
71B274700.06
72D274700.06
81B274950.06
82E274950.06
91B274040.06
92F274040.06
101C274060.05
102D274060.05
111C273520.05
112E273520.05
121C273370.05
122F273370.05
131D274100.06
132E274100.06
141D275450.06
142F275450.06
151E276240.05
152F276240.05
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 348 -
Rwork0.204 6239 -
all-6587 -
obs--89.29 %

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