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- PDB-1hg3: Crystal structure of tetrameric TIM from Pyrococcus woesei. -

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Basic information

Entry
Database: PDB / ID: 1hg3
TitleCrystal structure of tetrameric TIM from Pyrococcus woesei.
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / THERMOSTABILITY / PYROCOCCUS / TRIOSEPHOSPHATE ISOMERASE / TETRAMERIC
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function
Triosephosphate isomerase, archaeal / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I ...Triosephosphate isomerase, archaeal / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / 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
3-PHOSPHONOPROPANOIC ACID / Triosephosphate isomerase / Triosephosphate isomerase
Similarity search - Component
Biological speciesPYROCOCCUS WOESEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsWalden, H. / Bell, G.S. / Russell, R.J.M. / Siebers, B. / Hensel, R. / Taylor, G.L.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Tiny Tim: A Small, Tetrameric, Hyperthermostable Triosephosphate Isomerase
Authors: Walden, H. / Bell, G.S. / Russell, R.J.M. / Siebers, B. / Hensel, R. / Taylor, G.L.
History
DepositionDec 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: TRIOSEPHOSPHATE ISOMERASE
F: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,02216
Polymers189,7908
Non-polymers1,2328
Water6,233346
1
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5118
Polymers94,8954
Non-polymers6164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: TRIOSEPHOSPHATE ISOMERASE
F: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5118
Polymers94,8954
Non-polymers6164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.000, 89.100, 145.100
Angle α, β, γ (deg.)90.00, 92.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6803, -0.31876, 0.65999), (-0.31654, -0.68438, -0.65683), (0.66105, -0.65576, 0.36468)-23.834, 98.36513, 58.76599
2given(0.62704, -0.00728, -0.77895), (0.00306, -0.99993, 0.01181), (-0.77898, -0.00979, -0.62697)55.10153, 60.82224, 115.24031
3given(-0.93681, 0.32394, 0.13209), (0.32729, 0.67821, 0.65797), (0.12355, 0.65962, -0.74137)-6.37488, -36.65746, 96.46261
4given(0.99998, 0.00318, 0.00584), (-0.00319, 0.99999, 0.00161), (-0.00584, -0.00163, 0.99998)35.6823, 22.51346, 72.74033
5given(-0.67601, -0.32431, 0.66169), (-0.31563, -0.68397, -0.65769), (0.66587, -0.65346, 0.36001)12.35264, 121.03146, 131.69531
6given(0.62252, -0.01007, -0.78254), (0.0045, -0.99985, 0.01644), (-0.78259, -0.01376, -0.62239)91.66452, 83.0285, 187.68719
7given(-0.93656, 0.32639, 0.12778), (0.32599, 0.67712, 0.65973), (0.12881, 0.65953, -0.74056)30.10075, -14.10838, 169.0519

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE


Mass: 23723.691 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: 2-CARBOXYETHYLPHOSPHONIC ACID IN THE ACTIVE SITE / Source: (gene. exp.) PYROCOCCUS WOESEI (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: P95583, UniProt: P62003*PLUS, triose-phosphate isomerase
#2: Chemical
ChemComp-3PP / 3-PHOSPHONOPROPANOIC ACID / 2-CARBOXYETHYLPHOSPHONIC ACID


Mass: 154.058 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONVERTS D-GLYCERALDEHYDE 3-PHOSPHATE TO DIHYDROXY-ACETONE PHOSPHATE. PLAYS AN IMPORTANT ROLE IN ...CONVERTS D-GLYCERALDEHYDE 3-PHOSPHATE TO DIHYDROXY-ACETONE PHOSPHATE. PLAYS AN IMPORTANT ROLE IN SEVERAL METABOLIC PATHWAYS.
Sequence detailsTHE C-TERMINAL 15 RESIDUES LISTED IN THE SWISS-PROT ENTRY ARE INCORRECT. THE SWISS-PROT ENTRY WILL ...THE C-TERMINAL 15 RESIDUES LISTED IN THE SWISS-PROT ENTRY ARE INCORRECT. THE SWISS-PROT ENTRY WILL BE UPDATED SOON.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 %
Description: MAD DATA WERE USED TO DETERMINE THE STRUCTURE, CROSS- CRYSTAL AVERAGING AND PHASE EXTENSION USING IN-HOUSE DATA WERE USED IN REFINEMENT OF THE MODEL.
Crystal growpH: 4.6 / Details: 0.1M SODIUM ACETATE PH 4.0 AND 7% PEG 4000
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop / Details: Bell, G.S., (1998) Acta crystallog., D54, 1419.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mM2-carboxyethylphosphonic acid1reservoir
20.1 Msodium acetate1reservoir
37 %PEG40001reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9795,0.9796,0.9537
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.95371
ReflectionResolution: 3→30 Å / Num. obs: 25844 / % possible obs: 90.1 % / Observed criterion σ(I): 2.5 / Redundancy: 15 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.112 / % possible all: 89.7
Reflection
*PLUS
Num. measured all: 386571
Reflection shell
*PLUS
% possible obs: 89.7 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: NCS RESTRAINTS WERE USED THROUGHOUT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.286 5062 10 %RANDOM
Rwork0.254 ---
obs0.254 49927 98.1 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13232 0 72 346 13650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.8 Å
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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