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- PDB-4unk: Crystal structure of human triosephosphate isomerase (mutant N15D) -

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Basic information

Entry
Database: PDB / ID: 4unk
TitleCrystal structure of human triosephosphate isomerase (mutant N15D)
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / DEAMIDATION
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / canonical glycolysis / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / glycolytic process / 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: 2 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 Human Triosephosphate Isomerase (Mutant N15D)
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

Downloads & links

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,4312
Polymers53,4312
Non-polymers00
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-14.5 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.628, 70.714, 146.431
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: (-0.6361, 0.2254, -0.7379), (0.2398, -0.8513, -0.4667), (-0.7334, -0.4738, 0.4875)
Vector: 24.8328, 53.5893, 90.3233)

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Components

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


Mass: 26715.385 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 / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.12 Å3/Da / Density % sol: 41.54 % / Description: NONE
Crystal growpH: 8.5
Details: 200 MM AMMONIUM ACETATE, 100 MM TRIS PH 8.5, 25% V/VW/V POLYETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
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: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→48.81 Å / Num. obs: 34112 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 31.06 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JK2

2jk2


Resolution: 2→45.292 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 21.21 / Stereochemistry target values: ML
Details: RESIDUES 171-176 OF CHAIN B, KNOWN AS LOOP 6, ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2242 1723 5.1 %
Rwork0.1794 --
obs0.1817 34083 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 2→45.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 0 452 4122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073739
X-RAY DIFFRACTIONf_angle_d1.0245066
X-RAY DIFFRACTIONf_dihedral_angle_d13.9961351
X-RAY DIFFRACTIONf_chiral_restr0.069575
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.28161440.21862659X-RAY DIFFRACTION100
2.0589-2.12530.24821670.19332639X-RAY DIFFRACTION100
2.1253-2.20130.24531350.19412690X-RAY DIFFRACTION100
2.2013-2.28940.23451490.18912679X-RAY DIFFRACTION100
2.2894-2.39360.24731340.18672670X-RAY DIFFRACTION100
2.3936-2.51980.25771350.19062703X-RAY DIFFRACTION100
2.5198-2.67770.27621340.19242671X-RAY DIFFRACTION100
2.6777-2.88440.26741360.20122688X-RAY DIFFRACTION100
2.8844-3.17460.22921360.18372733X-RAY DIFFRACTION100
3.1746-3.63380.22551600.16752680X-RAY DIFFRACTION99
3.6338-4.57750.1681250.15112740X-RAY DIFFRACTION98
4.5775-45.3040.18911680.17472808X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.060.0179-0.00830.00930.00440.050.043-0.1141-0.11760.0081-0.0387-0.01010.0321-0.056-0.00770.0356-0.0412-0.01580.07320.03180.053834.9621.737298.7114
20.00020.0004-0.00080.00360.00070.0015-0.0230.01660.0372-0.0279-0.007-0.0234-0.03380.0027-0.00020.1314-0.02530.0370.0776-0.00230.164742.592641.140494.8092
30.23530.0234-0.03740.0473-0.06870.10240.06450.15260.04170.00940.01950.0056-0.07290.08670.2376-0.0049-0.06180.03670.1202-0.01890.052650.07828.767384.8692
40.02290.00870.01680.02520.01170.0634-0.01190.0949-0.1160.0019-0.06460.00490.0235-0.0172-0.1519-0.0585-0.0519-0.09160.1091-0.14520.127352.155916.909986.4397
50.0085-0.01140.00970.0216-0.01570.01380.04180.0053-0.09810.00660.0491-0.03190.0624-0.01430.13160.0578-0.0627-0.07880.0857-0.00540.284140.232411.162290.8101
60.05010.0628-0.03470.14320.0270.1942-0.0422-0.00460.0058-0.1071-0.0151-0.0107-0.13-0.0864-0.07550.14660.0911-0.03550.1975-0.10530.051125.558247.019699.7747
70.185-0.03220.14090.04630.01950.1948-0.19990.14410.2013-0.0477-0.1013-0.0559-0.35040.0422-0.58950.36060.0294-0.18960.12520.0455-0.023324.616456.507486.2938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 64 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 65 THROUGH 85 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 86 THROUGH 153 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 154 THROUGH 216 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 217 THROUGH 246 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 4 THROUGH 72 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 73 THROUGH 245 )

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