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- PDB-6bve: Triosephosphate isomerase of Synechocystis in complex with 2-Phos... -

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Basic information

Entry
Database: PDB / ID: 6bve
TitleTriosephosphate isomerase of Synechocystis in complex with 2-Phosphoglycolic acid
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM Synechocystis Redox Regulation
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsJimenez-Sandoval, P. / Castro-Torres, E. / Brieba, L.G.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Fronteras de la Ciencia 13 Mexico
CitationJournal: Front Mol Biosci / Year: 2018
Title: Structural Basis for the Limited Response to Oxidative and Thiol-Conjugating Agents by Triosephosphate Isomerase From the Photosynthetic BacteriaSynechocystis.
Authors: Castro-Torres, E. / Jimenez-Sandoval, P. / Fernandez-de Gortari, E. / Lopez-Castillo, M. / Baruch-Torres, N. / Lopez-Hidalgo, M. / Peralta-Castro, A. / Diaz-Quezada, C. / Sotelo-Mundo, R.R. ...Authors: Castro-Torres, E. / Jimenez-Sandoval, P. / Fernandez-de Gortari, E. / Lopez-Castillo, M. / Baruch-Torres, N. / Lopez-Hidalgo, M. / Peralta-Castro, A. / Diaz-Quezada, C. / Sotelo-Mundo, R.R. / Benitez-Cardoza, C.G. / Espinoza-Fonseca, L.M. / Ochoa-Leyva, A. / Brieba, L.G.
History
DepositionDec 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3086
Polymers52,9502
Non-polymers3584
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-55 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.880, 73.099, 85.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Triosephosphate isomerase / / TPI / Triose-phosphate isomerase


Mass: 26474.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: tpiA, tpi, slr0783 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59994, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate 6.5, 18 % w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.78→85.18 Å / Num. obs: 44327 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 15.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.027 / Rrim(I) all: 0.078 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.825.50.35524830.9030.1650.393100
9.08-85.187.10.02640910.010.02899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.78 Å55.47 Å
Translation1.78 Å55.47 Å

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Processing

Software
NameVersionClassification
d*TREKdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PHENIX1.12-2829-000refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BTM TRUNCATED TO POLY-A

1btm


Resolution: 1.78→55.471 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 17.21
RfactorNum. reflection% reflection
Rfree0.1902 2006 4.53 %
Rwork0.1543 --
obs0.156 44256 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.77 Å2 / Biso mean: 17.256 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 1.78→55.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 20 348 4002
Biso mean--17.29 22.93 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083807
X-RAY DIFFRACTIONf_angle_d0.8475189
X-RAY DIFFRACTIONf_chiral_restr0.058591
X-RAY DIFFRACTIONf_plane_restr0.006697
X-RAY DIFFRACTIONf_dihedral_angle_d3.1083068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.78-1.82460.23781410.192629443085
1.8246-1.87390.24021410.179429863127
1.8739-1.9290.19741410.159429563097
1.929-1.99130.2151420.151529833125
1.9913-2.06250.19321400.151429923132
2.0625-2.14510.21531430.15529973140
2.1451-2.24270.19291400.142729963136
2.2427-2.36090.16711410.148629923133
2.3609-2.50880.2211480.149130213169
2.5088-2.70260.19071410.156930023143
2.7026-2.97450.21991430.162130363179
2.9745-3.40490.20541440.157430483192
3.4049-4.28950.16121490.142330903239
4.2895-55.49830.15031520.154432073359

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