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- PDB-4unl: Crystal structure of a single mutant (N71D) of triosephosphate is... -

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Entry
Database: PDB / ID: 4unl
TitleCrystal structure of a single mutant (N71D) of triosephosphate isomerase from human
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / DEAMIDATION
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis / glycolytic process / gluconeogenesis / ubiquitin protein ligase binding / protein homodimerization activity / extracellular space / extracellular exosome / nucleus / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDeLaMora-DeLaMora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / Garcia-Torres, I. ...DeLaMora-DeLaMora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / Garcia-Torres, I. / Reyes-Vivas, H. / Oria-Hernandez, J.
CitationJournal: To be Published
Title: Crystal Structure of a Single Mutant (N71D) of Triosephosphate Isomerase from Human
Authors: Delamora-Delamora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / ...Authors: Delamora-Delamora, I. / Torres-Larios, A. / Enriquez-Flores, S. / Mendez, S.T. / Castillo-Villanueva, A. / Gomez-Manzo, S. / Lopez-Velazquez, G. / Marcial-Quino, J. / Torres-Arroyo, A. / Garcia-Torres, I. / Reyes-Vivas, H. / Oria-Hernandez, J.
History
DepositionMay 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,1432
Polymers53,1432
Non-polymers00
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-16.1 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.943, 72.841, 93.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8199, 0.2977, 0.489), (0.296, -0.5106, 0.8072), (0.49, 0.8066, 0.3306)
Vector: -1.2204, 16.91, -8.729)

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 26571.254 Da / Num. of mol.: 2 / Fragment: RESIDUES 39-286 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIL / References: UniProt: P60174, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.3 Å3/Da / Density % sol: 46.67 % / Description: NONE
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4,000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 28, 2010 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.5→39.28 Å / Num. obs: 71346 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.2
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK2

2jk2


Resolution: 1.5→39.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22564 3603 5.1 %RANDOM
Rwork0.19873 ---
obs0.2001 67516 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.537 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 0 350 4062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223751
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.955073
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1495480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77725.099151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71115638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6861516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212860
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_it2.151.52413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.89723857
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.26631338
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9284.51216
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 243 -
Rwork0.295 4895 -
obs--98.56 %

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