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- PDB-8dht: Crystal structure of a typeIII Rubisco -

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Basic information

Entry
Database: PDB / ID: 8dht
TitleCrystal structure of a typeIII Rubisco
ComponentsRibulose bisphosphate carboxylase
KeywordsLYASE / Rubisco / 3-phosphoglycerate / complex / PHOTOSYNTHESIS
Function / homology
Function and homology information


AMP catabolic process / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / oxidoreductase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, type III / 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
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / ACETATE ION / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsQingqiu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1-P30-GM124166-01A1 United States
CitationJournal: Proteins / Year: 2023
Title: Crystal structure of a type III Rubisco in complex with its product 3-phosphoglycerate.
Authors: Huang, Q. / Szebenyi, D.M.E.
History
DepositionJun 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,21527
Polymers194,7814
Non-polymers2,43323
Water25,3471407
1
A: Ribulose bisphosphate carboxylase
C: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,54513
Polymers97,3912
Non-polymers1,15411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-76 kcal/mol
Surface area27050 Å2
MethodPISA
2
B: Ribulose bisphosphate carboxylase
hetero molecules

D: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,67014
Polymers97,3912
Non-polymers1,27912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area11630 Å2
ΔGint-77 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.329, 116.206, 83.285
Angle α, β, γ (deg.)90.000, 96.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ribulose bisphosphate carboxylase / RuBisCO


Mass: 48695.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: rbcL, AF_1638 / Production host: Escherichia coli (E. coli)
References: UniProt: O28635, ribulose-bisphosphate carboxylase

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Non-polymers , 5 types, 1430 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1407 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 26% PEG4000 (w/v), 0.2M NaAc, 0.1M Tris-HCl, pH8.0 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.699→50 Å / Num. obs: 166579 / % possible obs: 100 % / Redundancy: 3.4 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Rsym value: 0.062 / Χ2: 0.619 / Net I/σ(I): 16.5
Reflection shellResolution: 1.699→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.087 / Num. unique obs: 8243 / CC1/2: 0.836 / CC star: 0.954 / Rpim(I) all: 0.247 / Rrim(I) all: 0.452 / Rsym value: 0.377 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KDO

3kdo


Resolution: 1.699→49.377 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1774 1998 1.2 %
Rwork0.1438 164514 -
obs0.1442 166512 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.01 Å2 / Biso mean: 21.4751 Å2 / Biso min: 9.36 Å2
Refinement stepCycle: final / Resolution: 1.699→49.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13652 0 148 1407 15207
Biso mean--23.7 32.6 -
Num. residues----1760
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6992-1.74170.23511420.19261159299
1.7417-1.78880.23781450.181311755100
1.7888-1.84140.21231400.161911639100
1.8414-1.90080.17591370.15611750100
1.9008-1.96880.18981510.146711759100
1.9688-2.04760.19061390.138411699100
2.0476-2.14080.15961440.138311761100
2.1408-2.25370.19291360.140211748100
2.2537-2.39490.17981500.142611750100
2.3949-2.57980.17621480.144111772100
2.5798-2.83930.17531390.143211764100
2.8393-3.25010.15981460.138511799100
3.2501-4.09450.16091410.127411802100
4.0945-49.3770.17411400.148411924100

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