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- PDB-4mkn: Crystal structure of chloroplastic triosephosphate isomerase from... -

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Basic information

Entry
Database: PDB / ID: 4mkn
TitleCrystal structure of chloroplastic triosephosphate isomerase from Chlamydomonas reinhardtii at 1.1 A of resolution
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM barrel / chloroplast
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chloroplast triosephosphate isomerase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsFermani, S. / Sciabolini, C. / Zaffagnini, M. / Lemaire, S.D.
CitationJournal: Mol Plant / Year: 2014
Title: High-Resolution Crystal Structure and Redox Properties of Chloroplastic Triosephosphate Isomerase from Chlamydomonas reinhardtii.
Authors: Zaffagnini, M. / Michelet, L. / Sciabolini, C. / Di Giacinto, N. / Morisse, S. / Marchand, C.H. / Trost, P. / Fermani, S. / Lemaire, S.D.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5067
Polymers28,7971
Non-polymers7096
Water4,504250
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,01114
Polymers57,5932
Non-polymers1,41812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6820 Å2
ΔGint-19 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.814, 93.211, 100.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-596-

HOH

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Components

#1: Protein Triosephosphate isomerase /


Mass: 28796.674 Da / Num. of mol.: 1 / Fragment: UNP residues 13-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TIM, TPIC, CHLREDRAFT_26265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S7Y5, triose-phosphate isomerase
#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 65% (v/v) MPD, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.885 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 1.1→46.61 Å / Num. all: 113723 / Num. obs: 111449 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 19.5
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.6 / Num. unique all: 16484 / Rsym value: 0.511 / % possible all: 92.7

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R2R

1r2r


Resolution: 1.1→46.61 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.357 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17717 5570 5 %RANDOM
Rwork0.16022 ---
all0.16109 108179 --
obs0.16109 105788 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.897 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.1→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 48 250 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6721.9712749
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7285266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26625.24482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72515322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.19157
X-RAY DIFFRACTIONr_chiral_restr0.1760.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4521.51272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35922036
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7753744
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9894.5706
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.099→1.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 408 -
Rwork0.246 7117 -
obs--90.27 %

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