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- PDB-7zuv: Crystal structure of Chlamydomonas reinhardtii chloroplastic sedo... -

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Basic information

Entry
Database: PDB / ID: 7zuv
TitleCrystal structure of Chlamydomonas reinhardtii chloroplastic sedoheptulose-1,7-bisphosphatase in reducing conditions
ComponentsFBPase domain-containing protein
KeywordsPHOTOSYNTHESIS / Sedoheptulose-1 / 7-bisphosphatase / calvin-benson cycle / chloroplast / Chlamydomonas reinhardtii
Function / homology
Function and homology information


sedoheptulose-bisphosphatase / reductive pentose-phosphate cycle / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / fructose 6-phosphate metabolic process / chloroplast / gluconeogenesis / metal ion binding / cytoplasm
Similarity search - Function
Sedoheptulose-1,7-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain
Similarity search - Domain/homology
Sedoheptulose-1,7-bisphosphatase, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsLe Moigne, T. / Robert, G.Q. / Lemaire, S.D. / Henri, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
Citation
Journal: Plant Physiol. / Year: 2024
Title: Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii.
Authors: Meloni, M. / Fanti, S. / Tedesco, D. / Gurrieri, L. / Trost, P. / Fermani, S. / Lemaire, S.D. / Zaffagnini, M. / Henri, J.
#1: Journal: Elife / Year: 2023
Title: Structure of the photosynthetic Calvin-Benson-Bassham sedoheptulose-1,7-bisphosphatase SBPase from the model microalga Chlamydomonas reinhardtii
Authors: Le Moigne, T. / Santoni, M. / Jomat, L. / Lemaire, S.D. / Zaffagnini, M. / Cheron, N. / Henri, J.
History
DepositionMay 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FBPase domain-containing protein
B: FBPase domain-containing protein
C: FBPase domain-containing protein
D: FBPase domain-containing protein
E: FBPase domain-containing protein
F: FBPase domain-containing protein
G: FBPase domain-containing protein
H: FBPase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,95810
Polymers289,7658
Non-polymers1922
Water00
1
A: FBPase domain-containing protein
hetero molecules

D: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,5373
Polymers72,4412
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4330 Å2
ΔGint-31 kcal/mol
Surface area22330 Å2
2
B: FBPase domain-containing protein
F: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,4412
Polymers72,4412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-16 kcal/mol
Surface area22140 Å2
3
C: FBPase domain-containing protein
H: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,4412
Polymers72,4412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-17 kcal/mol
Surface area21550 Å2
4
G: FBPase domain-containing protein
hetero molecules

E: FBPase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)72,5373
Polymers72,4412
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4320 Å2
ΔGint-34 kcal/mol
Surface area21070 Å2
Unit cell
Length a, b, c (Å)53.774, 163.462, 172.765
Angle α, β, γ (deg.)90.000, 91.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 78 through 116 or resid 131 through 386))
21(chain B and (resid 78 through 116 or resid 131 through 386))
31(chain C and (resid 78 through 116 or resid 131 through 386))
41(chain D and (resid 78 through 116 or resid 131 through 386))
51(chain E and (resid 78 through 116 or resid 131 through 386))
61(chain F and (resid 78 through 116 or resid 131 through 386))
71(chain G and (resid 78 through 116 or resid 131 through 386))
81(chain H and (resid 78 through 116 or resid 131 through 386))

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLY(chain A and (resid 78 through 116 or resid 131 through 386))AA78 - 11618 - 56
12LEULEU(chain A and (resid 78 through 116 or resid 131 through 386))AA131 - 38671 - 326
21GLYGLY(chain B and (resid 78 through 116 or resid 131 through 386))BB78 - 11618 - 56
22LEULEU(chain B and (resid 78 through 116 or resid 131 through 386))BB131 - 38671 - 326
31GLYGLY(chain C and (resid 78 through 116 or resid 131 through 386))CC78 - 11618 - 56
32LEULEU(chain C and (resid 78 through 116 or resid 131 through 386))CC131 - 38671 - 326
41GLYGLY(chain D and (resid 78 through 116 or resid 131 through 386))DD78 - 11618 - 56
42LEULEU(chain D and (resid 78 through 116 or resid 131 through 386))DD131 - 38671 - 326
51GLYGLY(chain E and (resid 78 through 116 or resid 131 through 386))EE78 - 11618 - 56
52LEULEU(chain E and (resid 78 through 116 or resid 131 through 386))EE131 - 38671 - 326
61GLYGLY(chain F and (resid 78 through 116 or resid 131 through 386))FF78 - 11618 - 56
62LEULEU(chain F and (resid 78 through 116 or resid 131 through 386))FF131 - 38671 - 326
71GLYGLY(chain G and (resid 78 through 116 or resid 131 through 386))GG78 - 11618 - 56
72LEULEU(chain G and (resid 78 through 116 or resid 131 through 386))GG131 - 38671 - 326
81GLYGLY(chain H and (resid 78 through 116 or resid 131 through 386))HH78 - 11618 - 56
82LEULEU(chain H and (resid 78 through 116 or resid 131 through 386))HH131 - 38671 - 326

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Components

#1: Protein
FBPase domain-containing protein / Sedoheptulose-1 / 7-bisphosphatase / chloroplastic


Mass: 36220.684 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_03g185550v5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2K3DY10, sedoheptulose-bisphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN
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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200mM lithium sulfate, 100mM tris-HCl pH7, 1 M sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.11→48.54 Å / Num. obs: 53456 / % possible obs: 99.65 % / Redundancy: 7 % / Biso Wilson estimate: 68.45 Å2 / CC1/2: 0.988 / CC star: 0.997 / Net I/σ(I): 8.54
Reflection shellResolution: 3.11→3.221 Å / Num. unique obs: 5213 / CC1/2: 0.479 / CC star: 0.805

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B2O

7b2o


Resolution: 3.11→48.54 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1984 3.71 %
Rwork0.1951 51462 -
obs0.1964 53446 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.25 Å2 / Biso mean: 68.4124 Å2 / Biso min: 26.97 Å2
Refinement stepCycle: final / Resolution: 3.11→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18704 0 10 0 18714
Biso mean--94.37 --
Num. residues----2451
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7136X-RAY DIFFRACTION7.569TORSIONAL
12B7136X-RAY DIFFRACTION7.569TORSIONAL
13C7136X-RAY DIFFRACTION7.569TORSIONAL
14D7136X-RAY DIFFRACTION7.569TORSIONAL
15E7136X-RAY DIFFRACTION7.569TORSIONAL
16F7136X-RAY DIFFRACTION7.569TORSIONAL
17G7136X-RAY DIFFRACTION7.569TORSIONAL
18H7136X-RAY DIFFRACTION7.569TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.180.36621370.33353460359793
3.18-3.270.35921450.279336353780100
3.27-3.370.27991380.263237233861100
3.37-3.480.2981350.247636103745100
3.48-3.60.29071500.243737513901100
3.6-3.740.25771410.225836523793100
3.74-3.910.24431390.201436913830100
3.91-4.120.23471530.192136983851100
4.12-4.380.2081400.174536563796100
4.38-4.720.18681380.152736983836100
4.72-5.190.21551370.154437033840100
5.19-5.940.23641470.178537303877100
5.94-7.480.21741440.185537053849100
7.48-48.540.15651400.161837503890100

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