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- PDB-5n9z: Rubisco from Thalassiosira hyalina -

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Basic information

Entry
Database: PDB / ID: 5n9z
TitleRubisco from Thalassiosira hyalina
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
KeywordsPHOTOSYNTHESIS / CARBON DIOXIDE FIXATION / PHOTORESPIRATION
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plastid / photosynthesis / 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, 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, 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, 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 / Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
Similarity search - Component
Biological speciesThalassiosira hyalina (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.899 Å
AuthorsAndersson, I. / Valegard, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
European UnionQLK3-CT-2002-01945 Sweden
Formas Sweden
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications.
Authors: Valegard, K. / Andralojc, P.J. / Haslam, R.P. / Pearce, F.G. / Eriksen, G.K. / Madgwick, P.J. / Kristoffersen, A.K. / van Lun, M. / Klein, U. / Eilertsen, H.C. / Parry, M.A.J. / Andersson, I.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: chem_comp / entity_poly / pdbx_seq_map_depositor_info
Item: _chem_comp.mon_nstd_flag / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 3.0May 15, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code

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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
I: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
H: Ribulose bisphosphate carboxylase large chain
O: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
F: Ribulose bisphosphate carboxylase large chain
N: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
D: Ribulose bisphosphate carboxylase large chain
M: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
B: Ribulose bisphosphate carboxylase large chain
P: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
C: Ribulose bisphosphate carboxylase large chain
J: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
E: Ribulose bisphosphate carboxylase large chain
K: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
G: Ribulose bisphosphate carboxylase large chain
L: Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,59553
Polymers563,32416
Non-polymers4,27137
Water55,9913108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area116910 Å2
ΔGint-426 kcal/mol
Surface area119780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.992, 219.986, 124.274
Angle α, β, γ (deg.)90.00, 118.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 16 molecules AHFDBCEGIONMPJKL

#1: Protein
Ribulose bisphosphate carboxylase large chain


Mass: 54432.645 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Thalassiosira hyalina (Diatom)
References: UniProt: A0A384E0M2*PLUS, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit


Mass: 15982.861 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Thalassiosira hyalina (Diatom) / References: UniProt: A0A384E0M3*PLUS

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Sugars , 1 types, 8 molecules

#4: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharideCarbohydrate / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2

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Non-polymers , 3 types, 3137 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3108 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 26% PRG4000, 0.1M HEPES pH 8.5, 0.1M sodium chloride, 0.005M magnesium chloride, 0.01M sodium hydrogen carbonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.899→97.9 Å / Num. obs: 432731 / % possible obs: 99.2 % / Redundancy: 8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.251 / Num. unique obs: 42903 / % possible all: 98.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX(1.10_2155: ???)refinement
Omodel building
RefinementResolution: 1.899→62.029 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 21704 5.02 %
Rwork0.1505 --
obs0.1521 432437 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→62.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39040 0 254 3108 42402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00740316
X-RAY DIFFRACTIONf_angle_d0.97354758
X-RAY DIFFRACTIONf_dihedral_angle_d12.77723597
X-RAY DIFFRACTIONf_chiral_restr0.0725927
X-RAY DIFFRACTIONf_plane_restr0.0057061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8993-1.92090.22255960.178612948X-RAY DIFFRACTION94
1.9209-1.94350.22157130.175913681X-RAY DIFFRACTION99
1.9435-1.96720.20977330.17113598X-RAY DIFFRACTION99
1.9672-1.99210.21727380.163113512X-RAY DIFFRACTION99
1.9921-2.01830.21417520.164113576X-RAY DIFFRACTION99
2.0183-2.0460.20997520.159213644X-RAY DIFFRACTION99
2.046-2.07520.20227260.158513612X-RAY DIFFRACTION99
2.0752-2.10620.20227150.157913732X-RAY DIFFRACTION99
2.1062-2.13910.20116910.156713604X-RAY DIFFRACTION99
2.1391-2.17420.20587530.157813621X-RAY DIFFRACTION99
2.1742-2.21160.20957380.155613648X-RAY DIFFRACTION99
2.2116-2.25190.20437340.15613683X-RAY DIFFRACTION99
2.2519-2.29520.18947260.15613697X-RAY DIFFRACTION99
2.2952-2.3420.18257060.152613730X-RAY DIFFRACTION99
2.342-2.3930.20076980.155513683X-RAY DIFFRACTION99
2.393-2.44860.19647510.158613702X-RAY DIFFRACTION99
2.4486-2.50990.18957360.15213675X-RAY DIFFRACTION99
2.5099-2.57770.20497590.156613751X-RAY DIFFRACTION99
2.5777-2.65360.18916850.154613756X-RAY DIFFRACTION99
2.6536-2.73920.19397120.151213797X-RAY DIFFRACTION100
2.7392-2.83710.18866970.158513798X-RAY DIFFRACTION100
2.8371-2.95070.18447560.159313742X-RAY DIFFRACTION100
2.9507-3.0850.18727300.158513767X-RAY DIFFRACTION100
3.085-3.24760.18747170.157513861X-RAY DIFFRACTION100
3.2476-3.45110.17596950.157213846X-RAY DIFFRACTION100
3.4511-3.71750.17097610.146313776X-RAY DIFFRACTION100
3.7175-4.09160.15247530.130513833X-RAY DIFFRACTION100
4.0916-4.68350.13766850.119413885X-RAY DIFFRACTION100
4.6835-5.89990.15337370.134913895X-RAY DIFFRACTION100
5.8999-62.06210.15237590.14413680X-RAY DIFFRACTION98

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