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- PDB-1mo0: Structural Genomics Of Caenorhabditis Elegans: Triose Phosphate I... -

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Basic information

Entry
Database: PDB / ID: 1mo0
TitleStructural Genomics Of Caenorhabditis Elegans: Triose Phosphate Isomerase
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / STRUCTURAL GENOMICS / Triose Phosphate Isomerase / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Glycolysis / Gluconeogenesis / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / myofibril / cell redox homeostasis ...Glycolysis / Gluconeogenesis / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / myofibril / cell redox homeostasis / determination of adult lifespan / 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
ACETATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.7 Å
AuthorsSymersky, J. / Li, S. / Finley, J. / Liu, Z.-J. / Qui, H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. ...Symersky, J. / Li, S. / Finley, J. / Liu, Z.-J. / Qui, H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. / Zhao, J. / Thomas, W. / Nagy, L.A. / Sha, B. / DeLucas, L.J. / Wang, B.-C. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
Journal: Proteins / Year: 2003
Title: Structural genomics of Caenorhabditis elegans: triosephosphate isomerase
Authors: Symersky, J. / Li, S. / Carson, M. / Luo, M.
#1: Journal: To be published
Title: Structural genomics of Caenorhabditis elegans: The structure of the cytoskeleton-associated protein (CAP-Gly) domain of F53F4.3.
Authors: Li, S. / Finley, J. / Liu, Z.-J. / Qui, H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. / Zhao, J. / Thomas, W. / Nagy, L.A. / Sha, B. / DeLucas, L.J. / Wang, B.-C. / Luo, M.
History
DepositionSep 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)60,3589
Polymers59,7602
Non-polymers5987
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-96 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.399, 64.373, 105.706
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Triosephosphate isomerase / E.C.5.3.1.1 / TIM


Mass: 29880.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: PDEST 17.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10657, triose-phosphate isomerase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.063 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2 M AMMONIUM SULFATE, 50 mM SODIUM ACETATE at pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Mammonium sulfate1reservoir
250 mMsodium acetate1reservoirpH5.5
316 mg/mlprotein1drop
415 mMHEPES1droppH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.976
DetectorDetector: IMAGE PLATE / Date: Jun 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→29.6 Å / Num. all: 49911 / Num. obs: 49911 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 14.6 Å2 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 86.5 % / Redundancy: 2.64 % / Rsym value: 0.206
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 29.6 Å / Num. obs: 49994 / Num. measured all: 174695 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RESOLVEmodel building
CNS1refinement
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAS
Starting model: THE STRUCTURE WAS SOLVED USING THE DATA COLLECTED ON R-AXIS IV WITH CU_KA RADIATION TO 2-A RESOLUTION. THE CRYSTAL WAS SOAKED WITH POTASSIUM IODIDE PRIOR DATA COLLECTION

Resolution: 1.7→29.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2496 5 %RANDOM
Rwork0.183 ---
obs0.183 49911 92.6 %-
all-49911 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8849 Å2 / ksol: 0.384014 e/Å3
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-3.76 Å2
2---4.84 Å20 Å2
3---7.07 Å2
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 33 461 4295
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1441.5
X-RAY DIFFRACTIONc_mcangle_it1.8382
X-RAY DIFFRACTIONc_scbond_it1.6132
X-RAY DIFFRACTIONc_scangle_it2.5862.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 394 5 %
Rwork0.238 7413 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ACT.PARAMACT.TOPOL
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 29.6 Å / Num. reflection obs: 49994 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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