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- PDB-8thm: Beta carbonic anhydrase from the carboxysome of Cyanobium PCC 7001 -

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Basic information

Entry
Database: PDB / ID: 8thm
TitleBeta carbonic anhydrase from the carboxysome of Cyanobium PCC 7001
ComponentsCarboxysome shell carbonic anhydrase
KeywordsPHOTOSYNTHESIS / beta-carbonic anhydrase / carboxysome / cyanobacteria / RuBP activated / LYASE
Function / homology
Function and homology information


carboxysome / carbon fixation / carbonic anhydrase / carbonate dehydratase activity / metal ion binding
Similarity search - Function
Carboxysome shell carbonic anhydrase / Carboxysome shell carbonic anhydrase, N-terminal / Carboxysome shell carbonic anhydrase, C-terminal / Carboxysome Shell Carbonic Anhydrase, C-terminal
Similarity search - Domain/homology
BICARBONATE ION / CARBON DIOXIDE / RIBULOSE-1,5-DIPHOSPHATE / Carboxysome shell carbonic anhydrase
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPulsford, S.B. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Alpha-cyanobacterial carbonic anhydrase is allosterically regulated by the Rubisco substrate Ribulose 1,5-bisphosphate (RuBP)
Authors: Pulsford, S.B. / Outram, M.A. / Forster, B. / Jackson, C.J. / Rhodes, T. / Williams, S.J. / Price, G.D. / Badger, M.R. / Long, B.M.
History
DepositionJul 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxysome shell carbonic anhydrase
B: Carboxysome shell carbonic anhydrase
C: Carboxysome shell carbonic anhydrase
D: Carboxysome shell carbonic anhydrase
E: Carboxysome shell carbonic anhydrase
F: Carboxysome shell carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,01054
Polymers307,8516
Non-polymers5,15948
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26470 Å2
ΔGint-717 kcal/mol
Surface area102150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.314, 181.848, 190.057
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Carboxysome shell carbonic anhydrase / Carbonic anhydrase / Carboxysome shell protein CsoS3


Mass: 51308.566 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobium sp. PCC 7001 (bacteria) / Gene: CPCC7001_23 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5ILN4, carbonic anhydrase
#6: Sugar
ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE / Ribulose 1,5-bisphosphate


Type: saccharideCarbohydrate / Mass: 310.090 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H12O11P2 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 7 types, 815 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#8: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CHO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS (pH 6.5), 21% PEG 3350, 15% Ethylene glycol

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→48.48 Å / Num. obs: 160617 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.077 / Rrim(I) all: 0.271 / Χ2: 1.02 / Net I/σ(I): 8.1 / Num. measured all: 1970240
Reflection shellResolution: 2.3→2.34 Å / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 5.093 / Num. measured all: 100213 / Num. unique obs: 7868 / CC1/2: 0.297 / Rpim(I) all: 1.468 / Rrim(I) all: 5.302 / Χ2: 1.04 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.51 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 7990 4.98 %
Rwork0.193 --
obs0.1958 160413 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21655 0 274 774 22703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122753
X-RAY DIFFRACTIONf_angle_d1.04130974
X-RAY DIFFRACTIONf_dihedral_angle_d23.8458245
X-RAY DIFFRACTIONf_chiral_restr0.0633345
X-RAY DIFFRACTIONf_plane_restr0.0074133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.36092360.33145022X-RAY DIFFRACTION100
2.33-2.350.38642300.33055047X-RAY DIFFRACTION100
2.35-2.380.39282770.31865023X-RAY DIFFRACTION100
2.38-2.410.37972550.31355032X-RAY DIFFRACTION100
2.41-2.440.39192750.30994982X-RAY DIFFRACTION100
2.44-2.480.34682700.29885062X-RAY DIFFRACTION100
2.48-2.510.3422600.28774992X-RAY DIFFRACTION100
2.51-2.550.31642510.27455095X-RAY DIFFRACTION100
2.55-2.590.34972650.27125013X-RAY DIFFRACTION100
2.59-2.630.29482270.26555084X-RAY DIFFRACTION100
2.63-2.680.34012400.2595098X-RAY DIFFRACTION100
2.68-2.730.34792980.25614982X-RAY DIFFRACTION100
2.73-2.780.33172630.2555063X-RAY DIFFRACTION100
2.78-2.840.30482460.24785093X-RAY DIFFRACTION100
2.84-2.90.31412570.24455052X-RAY DIFFRACTION100
2.9-2.970.3292600.24575068X-RAY DIFFRACTION100
2.97-3.040.28632460.23345066X-RAY DIFFRACTION100
3.04-3.120.29882560.23075066X-RAY DIFFRACTION100
3.12-3.210.27742610.2245077X-RAY DIFFRACTION100
3.21-3.320.29742660.21585070X-RAY DIFFRACTION100
3.32-3.440.27222890.20025080X-RAY DIFFRACTION100
3.44-3.570.2462860.19755058X-RAY DIFFRACTION100
3.57-3.740.23962800.17675097X-RAY DIFFRACTION100
3.74-3.930.20472920.16095059X-RAY DIFFRACTION100
3.93-4.180.20892950.15235100X-RAY DIFFRACTION100
4.18-4.50.18352980.13685078X-RAY DIFFRACTION100
4.5-4.950.18662580.13325183X-RAY DIFFRACTION100
4.95-5.670.19573100.14325126X-RAY DIFFRACTION100
5.67-7.140.22752810.16385209X-RAY DIFFRACTION100
7.14-47.510.18092620.14885446X-RAY DIFFRACTION100

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