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- PDB-2ybv: STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS -

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Basic information

Entry
Database: PDB / ID: 2ybv
TitleSTRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS
Components
  • RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
  • RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
KeywordsLYASE / CO2/O2 SPECIFICITY / CARBON DIOXIDE FIXATION / PHOTOSYNTHESIS / THERMOSTABILITY / PHOTORESPIRATION / MONOOXYGENASE / HYDROXYLATION / OXIDOREDUCTASE / RUBISCO / CHLOROPLAST / CALVIN CYCLE / THERMOPHILIC CYANOBACTERIA
Function / homology
Function and homology information


photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding / cytoplasm
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
Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit
Similarity search - Component
Biological speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTerlecka, B. / Wilhelmi, V. / Bialek, W. / Gubernator, B. / Szczepaniak, A. / Hofmann, E.
CitationJournal: To be Published
Title: Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase from Thermosynechococcus Elongatus
Authors: Terlecka, B. / Wilhelmi, V. / Bialek, W. / Gubernator, B. / Szczepaniak, A. / Hofmann, E.
History
DepositionMar 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "OB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
B: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
C: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
D: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
E: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
F: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
G: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
H: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
I: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
J: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
K: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
L: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
M: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
N: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
O: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
P: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)537,26131
Polymers536,72916
Non-polymers53215
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79650 Å2
ΔGint-335.3 kcal/mol
Surface area124090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.480, 163.470, 163.540
Angle α, β, γ (deg.)90.00, 108.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
12B
22D
32F
42H
52J
62L
72N
82P

NCS domain segments:

Component-ID: 1 / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA23 - 45923 - 459
21THRTHRCC23 - 45923 - 459
31THRTHREE23 - 45923 - 459
41THRTHRGG23 - 45923 - 459
51THRTHRII23 - 45923 - 459
61THRTHRKK23 - 45923 - 459
71THRTHRMM23 - 45923 - 459
81THRTHROO23 - 45923 - 459
12ALAALABB31 - 3931 - 39
22ALAALADD31 - 3931 - 39
32ALAALAFF31 - 3931 - 39
42ALAALAHH31 - 3931 - 39
52ALAALAJJ31 - 3931 - 39
62ALAALALL31 - 3931 - 39
72ALAALANN31 - 3931 - 39
82ALAALAPP31 - 3931 - 39

NCS ensembles :
ID
1
2

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Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN


Mass: 53091.324 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA]
References: UniProt: Q8DIS5, ribulose-bisphosphate carboxylase
#2: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT


Mass: 13999.818 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA]
References: UniProt: Q8DIS7, ribulose-bisphosphate carboxylase
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.72 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7
Details: 5% PEG8000, 20% PEG200, 10% GLYCEROL, 100MM HEPES, PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9919
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2007 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.3→39 Å / Num. obs: 253864 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.11
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RUB

3rub


Resolution: 2.3→39.84 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 5.896 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23167 12992 5.1 %RANDOM
Rwork0.19577 ---
obs0.19763 240880 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.196 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20.69 Å2
2---0.77 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33736 0 15 832 34583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02234572
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.94846880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6354224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88123.6491688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.816155664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.53815256
X-RAY DIFFRACTIONr_chiral_restr0.1260.25024
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02126744
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.521160
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.756234008
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.661313412
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2794.512872
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1712tight positional0.060.05
12C1712tight positional0.060.05
13E1712tight positional0.050.05
14G1712tight positional0.050.05
15I1712tight positional0.060.05
16K1712tight positional0.060.05
17M1712tight positional0.060.05
18O1712tight positional0.060.05
21B36tight positional0.040.05
22D36tight positional0.040.05
23F36tight positional0.030.05
24H36tight positional0.040.05
25J36tight positional0.040.05
26L36tight positional0.040.05
27N36tight positional0.040.05
28P36tight positional0.050.05
11A1636medium positional0.110.5
12C1636medium positional0.10.5
13E1636medium positional0.10.5
14G1636medium positional0.090.5
15I1636medium positional0.090.5
16K1636medium positional0.080.5
17M1636medium positional0.110.5
18O1636medium positional0.080.5
21B33medium positional0.050.5
22D33medium positional0.050.5
23F33medium positional0.050.5
24H33medium positional0.060.5
25J33medium positional0.060.5
26L33medium positional0.060.5
27N33medium positional0.060.5
28P33medium positional0.060.5
11A1712tight thermal0.210.5
12C1712tight thermal0.190.5
13E1712tight thermal0.210.5
14G1712tight thermal0.230.5
15I1712tight thermal0.220.5
16K1712tight thermal0.220.5
17M1712tight thermal0.210.5
18O1712tight thermal0.210.5
21B36tight thermal0.150.5
22D36tight thermal0.10.5
23F36tight thermal0.240.5
24H36tight thermal0.180.5
25J36tight thermal0.160.5
26L36tight thermal0.190.5
27N36tight thermal0.180.5
28P36tight thermal0.10.5
11A1636medium thermal0.222
12C1636medium thermal0.212
13E1636medium thermal0.232
14G1636medium thermal0.212
15I1636medium thermal0.232
16K1636medium thermal0.22
17M1636medium thermal0.212
18O1636medium thermal0.222
21B33medium thermal0.112
22D33medium thermal0.12
23F33medium thermal0.182
24H33medium thermal0.142
25J33medium thermal0.172
26L33medium thermal0.122
27N33medium thermal0.12
28P33medium thermal0.112
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.249 18689 -
Rfree-0 -
obs--100 %

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