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- PDB-6zxt: High resolution crystal structure of chloroplastic ribose-5-phosp... -

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Basic information

Entry
Database: PDB / ID: 6zxt
TitleHigh resolution crystal structure of chloroplastic ribose-5-phosphate isomerase from Chlamydomonas reinhardtii
ComponentsRibose-5-phosphate isomerase
KeywordsISOMERASE / Ribose-5-phosphate / Rossmann fold / enzyme / chloroplast / photosynthese / Chlamydomonas
Function / homology: / Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / NagB/RpiA transferase-like / ribose-5-phosphate isomerase
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsLe Moigne, T. / Crozet, P. / Lemaire, S.D. / Henri, J.
CitationJournal: Int J Mol Sci / Year: 2020
Title: High-Resolution Crystal Structure of Chloroplastic Ribose-5-Phosphate Isomerase from Chlamydomonas reinhardtii -An Enzyme Involved in the Photosynthetic Calvin-Benson Cycle.
Authors: Le Moigne, T. / Crozet, P. / Lemaire, S.D. / Henri, J.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Ribose-5-phosphate isomerase
B: Ribose-5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,99012
Polymers55,1762
Non-polymers81410
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-135 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.152, 63.952, 80.909
Angle α, β, γ (deg.)90.000, 96.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribose-5-phosphate isomerase


Mass: 27587.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RPI1, CHLRE_03g187450v5, CHLREDRAFT_55838 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A8IRQ1, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1141.57
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
293.151evaporationammonium sulfate
293.152evaporationammonium sulfate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.4→44.89 Å / Num. obs: 89012 / % possible obs: 99.62 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0519 / Rpim(I) all: 0.02114 / Rrim(I) all: 0.05611 / Net I/σ(I): 20.58
Reflection shellResolution: 1.404→1.454 Å / Rmerge(I) obs: 1.272 / Num. unique obs: 8611 / CC1/2: 0.382

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MC0

6mc0


Resolution: 1.4→44.89 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1764 2000 2.25 %
Rwork0.1577 86983 -
obs0.1581 88983 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.33 Å2 / Biso mean: 26.943 Å2 / Biso min: 13.63 Å2
Refinement stepCycle: final / Resolution: 1.4→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 47 511 4121
Biso mean--49.89 35.49 -
Num. residues----474
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 (%)
1.4-1.440.38831360.37245886602295
1.44-1.480.34171430.320362066349100
1.48-1.520.28811420.274262076349100
1.52-1.570.26531430.220861976340100
1.57-1.630.21341420.188962106352100
1.63-1.690.1951430.180562166359100
1.69-1.770.19071430.172462176360100
1.77-1.860.23391430.166962366379100
1.86-1.980.17611430.152962336376100
1.98-2.130.15831440.146562436387100
2.13-2.350.16531430.144162246367100
2.35-2.690.18741450.14562626407100
2.69-3.380.17261440.145362736417100
3.38-44.890.13781460.143263736519100

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