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- PDB-1r2s: CRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 1r2s
TitleCRYSTAL STRUCTURE OF RABBIT MUSCLE TRIOSEPHOSPHATE ISOMERASE
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / Closed loop conformation in the ligand-free state / Conformational heterogeneity / Tim-barrel
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / gluconeogenesis / ubiquitin protein ligase binding ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / gluconeogenesis / ubiquitin protein ligase binding / protein homodimerization activity / 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 speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsAparicio, R. / Ferreira, S.T. / Polikarpov, I.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Closed conformation of the active site loop of rabbit muscle triosephosphate isomerase in the absence of substrate: evidence of conformational heterogeneity.
Authors: Aparicio, R. / Ferreira, S.T. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Preliminary X-ray diffraction studies of rabbit muscle triose phosphate isomerase (TIM)
Authors: Aparicio, R. / Ferreira, S.T. / Polikarpov, I. / Leite, N.R.
History
DepositionSep 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)106,6344
Polymers106,6344
Non-polymers00
Water2,432135
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)53,3172
Polymers53,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-17 kcal/mol
Surface area20030 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)53,3172
Polymers53,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-18 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.229, 80.289, 174.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
12A
22C

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGGLUGLUAA4 - 1404 - 140
211ARGARGGLUGLUBB4 - 1404 - 140
311ARGARGGLUGLUCC4 - 1404 - 140
411ARGARGGLUGLUDD4 - 1404 - 140
521ILEILEALAALAAA150 - 246150 - 246
621ILEILEALAALABB150 - 246150 - 246
721ILEILEALAALACC150 - 246150 - 246
821ILEILEALAALADD150 - 246150 - 246
112LYSLYSVALVALAA141 - 149141 - 149
212LYSLYSVALVALCC141 - 149141 - 149

NCS ensembles :
ID
1
2
DetailsThe asymmetric unit contains two physiologically active dimers formed by chains {A,B} and {C,D}

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Components

#1: Protein
Triosephosphate isomerase / TIM


Mass: 26658.398 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00939, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
124 %(w/v)PEG40001reservoir
20.2 M1reservoirMgCl2
30.1 MTris-HCl1reservoirpH8.5
41.1 MDMSO1reservoir
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.37 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 22, 1998 / Details: Mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 2.85→13.5 Å / Num. all: 20988 / Num. obs: 20064 / % possible obs: 80.9 % / Observed criterion σ(I): 2 / Redundancy: 1.93 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.11
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 1.31 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 2.55 / Num. unique all: 1617 / % possible all: 58.3
Reflection
*PLUS
Lowest resolution: 14 Å
Reflection shell
*PLUS
Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 1.99

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HTI

1hti


Resolution: 2.85→13.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.779 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21194 1026 5.1 %RANDOM
Rwork0.17196 ---
all0.17399 ---
obs0.17399 18929 81.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.69 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.85→13.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7469 0 0 135 7604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217622
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.94510322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5145983
X-RAY DIFFRACTIONr_chiral_restr0.0890.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025680
X-RAY DIFFRACTIONr_nbd_refined0.210.22748
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5550.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7050.23
X-RAY DIFFRACTIONr_mcbond_it0.5541.54882
X-RAY DIFFRACTIONr_mcangle_it1.09127842
X-RAY DIFFRACTIONr_scbond_it1.48832740
X-RAY DIFFRACTIONr_scangle_it2.7234.52480
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1747tight positional0.050.05
12B1747tight positional0.050.05
13C1747tight positional0.060.05
14D1747tight positional0.060.05
21A75tight positional0.050.05
11A1747tight thermal0.070.5
12B1747tight thermal0.080.5
13C1747tight thermal0.10.5
14D1747tight thermal0.10.5
21A75tight thermal0.090.5
LS refinement shellResolution: 2.85→2.921 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 59
Rwork0.231 948
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)
12.02640.4088-0.05694.23211.00892.66620.16-0.3263-0.68450.9299-0.21990.0890.4975-0.01290.05990.522-0.04090.03140.39840.17290.444814.71865.901932.7339
22.33450.9302-0.36793.2612-0.15853.26350.2332-0.51470.31510.838-0.22830.2444-0.51330.1471-0.00490.4504-0.11350.09640.3889-0.1140.254120.00340.48532.1133
32.1810.60730.60132.66470.41661.3918-0.16080.15770.5258-0.10160.00940.1811-0.1589-0.01780.15140.068-0.0067-0.03090.11450.05610.202718.802763.3435-7.0579
41.98340.07970.28432.4596-0.66441.7880.02640.1417-0.289-0.2860.00770.04550.26640.0496-0.03410.0480.0167-0.01080.091-0.07790.067217.202428.464-5.4748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2482 - 248
2X-RAY DIFFRACTION2BB3 - 2483 - 248
3X-RAY DIFFRACTION3CC2 - 2482 - 248
4X-RAY DIFFRACTION4DD2 - 2482 - 248
Refinement
*PLUS
Lowest resolution: 14 Å / % reflection Rfree: 5 % / Rfactor obs: 0.174 / Rfactor Rfree: 0.2119 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.358
LS refinement shell
*PLUS
Highest resolution: 2.85 Å / Lowest resolution: 2.92 Å

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