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- PDB-6hun: Dimeric Archeal Rubisco from Hyperthermus butylicus -

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Basic information

Entry
Database: PDB / ID: 6hun
TitleDimeric Archeal Rubisco from Hyperthermus butylicus
ComponentsRibulose bisphosphate carboxylaseRuBisCO
KeywordsPHOTOSYNTHESIS / ribulose-1 / 5-bisphosphate carboxylase oxygenase / rubisco / thermal stability / Hyperthermus butylicus
Function / homology
Function and homology information


AMP catabolic process / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / oxidoreductase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, type III / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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 ...Ribulose bisphosphate carboxylase, type III / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain / RuBisCO large subunit, N-terminal domain / 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
Similarity search - Component
Biological speciesHyperthermus butylicus DSM 5456 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsKeown, J.R. / Bundela, R. / Pearce, F.G.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structure of a hyperthermostable dimeric archaeal Rubisco from Hyperthermus butylicus.
Authors: Bundela, R. / Keown, J. / Watkin, S. / Pearce, F.G.
History
DepositionOct 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3032
Polymers51,2631
Non-polymers401
Water2,288127
1
A: Ribulose bisphosphate carboxylase
hetero molecules

A: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6054
Polymers102,5252
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area6950 Å2
ΔGint-58 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.412, 69.866, 94.494
Angle α, β, γ (deg.)90.000, 112.620, 90.000
Int Tables number5
Space group name H-MI121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21A-658-

HOH

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Components

#1: Protein Ribulose bisphosphate carboxylase / RuBisCO / RuBisCO


Mass: 51262.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyperthermus butylicus DSM 5456 (archaea)
Gene: rbcL, Hbut_0503 / Production host: Escherichia coli (E. coli)
References: UniProt: A2BK54, ribulose-bisphosphate carboxylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M CaCl2, 20% (w/v) PEG6000, and 100 mM sodium acetate/acetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→49.31 Å / Num. obs: 41694 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.37 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.8430.22323460.9340.1530.27294.1
9.01-49.312.80.0543560.9890.0370.06697.7

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GEH

1geh


Resolution: 1.802→43.613 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.56
RfactorNum. reflection% reflection
Rfree0.2163 2054 4.93 %
Rwork0.1789 --
obs0.1807 41684 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.61 Å2 / Biso mean: 46.5897 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: final / Resolution: 1.802→43.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 1 127 3497
Biso mean--44.43 42.1 -
Num. residues----428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8018-1.84370.26041520.23892495264795
1.8437-1.88980.251510.220326102761100
1.8898-1.94090.25161300.216626342764100
1.9409-1.9980.25681410.225726312772100
1.998-2.06250.28461240.217626652789100
2.0625-2.13620.25781440.214826522796100
2.1362-2.22170.24761330.209126292762100
2.2217-2.32290.23971360.198226572793100
2.3229-2.44530.2511440.191726632807100
2.4453-2.59850.22271220.18626392761100
2.5985-2.79910.21431290.188726882817100
2.7991-3.08070.22571320.192726412773100
3.0807-3.52630.23261430.17752640278399
3.5263-4.44210.17771370.15062668280599
4.4421-43.62530.17981360.1482718285499
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)
11.5427-0.0104-0.6163.1235-0.04262.49880.2293-0.81810.06160.13340.0381-0.7018-0.0531.3957-0.02820.1937-0.0202-0.16970.6613-0.02590.259732.9786-0.2478-33.1479
22.7502-0.3957-1.57052.76690.0523.17670.4607-0.01640.35930.4098-0.1470.5482-0.3602-0.3196-0.12010.2561-0.01920.10490.1762-0.03290.34046.071110.0302-32.7413
31.65440.0148-1.00630.7309-0.96572.38360.16140.1114-0.14490.54610.04270.83990.2004-0.8709-0.22760.5509-0.23010.27270.5449-0.07030.7452-8.60530.7325-22.127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 149 )A9 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 357 )A150 - 357
3X-RAY DIFFRACTION3chain 'A' and (resid 358 through 440 )A358 - 440

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