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- PDB-7b2n: Crystal structure of Chlamydomonas reinhardtii chloroplastic Fruc... -

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Basic information

Entry
Database: PDB / ID: 7b2n
TitleCrystal structure of Chlamydomonas reinhardtii chloroplastic Fructose bisphosphate aldolase
ComponentsFructose-bisphosphate aldolase 1, chloroplastic
KeywordsPHOTOSYNTHESIS / Fructose bisphosphate aldolase / Chlamydomonas reinhardtii / glyceraldehyde-3-phosphate / dihydroxyacetone phosphate / fructose-1 / 6-bisphosphate / Calvin-benson cycle
Function / homologyFructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / chloroplast / glycolytic process / Aldolase-type TIM barrel / Fructose-bisphosphate aldolase 1, chloroplastic
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLe Moigne, T. / Lemaire, S.D. / Henri, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)JCJC CALVINTERACT ANR-19-CE11-0009 France
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii.
Authors: Le Moigne, T. / Sarti, E. / Nourisson, A. / Zaffagnini, M. / Carbone, A. / Lemaire, S.D. / Henri, J.
History
DepositionNov 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase 1, chloroplastic
B: Fructose-bisphosphate aldolase 1, chloroplastic
C: Fructose-bisphosphate aldolase 1, chloroplastic
D: Fructose-bisphosphate aldolase 1, chloroplastic
E: Fructose-bisphosphate aldolase 1, chloroplastic
F: Fructose-bisphosphate aldolase 1, chloroplastic
G: Fructose-bisphosphate aldolase 1, chloroplastic
H: Fructose-bisphosphate aldolase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,36538
Polymers315,5448
Non-polymers2,82130
Water17,817989
1
A: Fructose-bisphosphate aldolase 1, chloroplastic
B: Fructose-bisphosphate aldolase 1, chloroplastic
D: Fructose-bisphosphate aldolase 1, chloroplastic
H: Fructose-bisphosphate aldolase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,15219
Polymers157,7724
Non-polymers1,38015
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-233 kcal/mol
Surface area48210 Å2
MethodPISA
2
C: Fructose-bisphosphate aldolase 1, chloroplastic
E: Fructose-bisphosphate aldolase 1, chloroplastic
F: Fructose-bisphosphate aldolase 1, chloroplastic
G: Fructose-bisphosphate aldolase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,21319
Polymers157,7724
Non-polymers1,44115
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-252 kcal/mol
Surface area47990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.493, 251.068, 126.411
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Fructose-bisphosphate aldolase 1, chloroplastic


Mass: 39442.965 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ALDCHL, CHLREDRAFT_24459 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q42690, fructose-bisphosphate aldolase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.5 M Ammonium sulfate, 6% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.983995275547 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983995275547 Å / Relative weight: 1
ReflectionResolution: 2.36→46.67 Å / Num. obs: 138497 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 40.19 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.34
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.495 / Num. unique obs: 13155 / % possible all: 94.4

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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: PHYRE2 MODEL

Resolution: 2.36→46.67 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 1984 1.43 %
Rwork0.203 136436 -
obs0.203 138420 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.28 Å2 / Biso mean: 46.78 Å2 / Biso min: 15.88 Å2
Refinement stepCycle: final / Resolution: 2.36→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20266 0 146 989 21401
Biso mean--68.59 43.18 -
Num. residues----2649
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 (%)
2.36-2.420.34961310.32449009914092
2.42-2.490.39081410.292798149955100
2.49-2.560.31951430.266297239866100
2.56-2.640.29371380.249597959933100
2.64-2.740.28221430.241998169959100
2.74-2.850.28641450.247497799924100
2.85-2.970.29491420.233597719913100
2.97-3.130.29671420.221797869928100
3.13-3.330.25671450.217698389983100
3.33-3.580.24291420.200197669908100
3.58-3.940.24521420.179398109952100
3.94-4.520.19791440.164298169960100
4.52-5.690.22091410.16498229963100
5.69-46.670.2051450.1751989110036100

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