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- PDB-2j24: The functional role of the conserved active site proline of trios... -

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Basic information

Entry
Database: PDB / ID: 2j24
TitleThe functional role of the conserved active site proline of triosephosphate isomerase
ComponentsTRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
KeywordsISOMERASE / PROTEIN ENGINEERING / FATTY ACID BIOSYNTHESIS / GLUCONEOGENESIS / LIPID SYNTHESIS / PENTOSE SHUNT / POINT MUTATION / LOOP7 / GLYCOSOME / TIM-BARREL
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytoplasm / 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, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCasteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2006
Title: Functional Role of the Conserved Active Site Proline of Triosephosphate Isomerase.
Authors: Casteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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, GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL


Theoretical massNumber of molelcules
Total (without water)53,6802
Polymers53,6802
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-19 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.500, 43.720, 71.270
Angle α, β, γ (deg.)80.49, 79.61, 64.66
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 2 - 250 / Label seq-ID: 2 - 250

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-1, -0.000139, 0.001548), (-0.000144, 1, -0.003005), (-0.001548, -0.003005, -1)
Vector: 8.326, -0.06445, -36.06)

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Components

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


Mass: 26839.795 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04789, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 168 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 168 TO ALA

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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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growpH: 7
Details: WELL SOLUTION: 0.1 M TEA PH 7.0, 27% PEG 2K MME AND 0.2 M KSCN PROTEIN SOLUTION: 11 MG/ML PROTEIN, 0.02 M TRIS/HCL PH 7.0, 0.1 M NACL, 1 MM DTT, 1 MM EDTA AND 1 MM NAN3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2004 / Details: MONTEL MIRRORS
RadiationMonochromator: MONTEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 22102 / % possible obs: 94.5 % / Redundancy: 2.65 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.63 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 8.67 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIM

5tim


Resolution: 2.1→19.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.883 / SU B: 10.282 / SU ML: 0.15 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1106 5 %RANDOM
Rwork0.149 ---
obs0.153 20995 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.12 Å20.21 Å2
2--0.15 Å2-0.79 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 0 399 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223874
X-RAY DIFFRACTIONr_bond_other_d0.0010.023631
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9385260
X-RAY DIFFRACTIONr_angle_other_deg0.8838435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.22824.581155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43115668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9641519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02750
X-RAY DIFFRACTIONr_nbd_refined0.2140.2931
X-RAY DIFFRACTIONr_nbd_other0.1920.24018
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21951
X-RAY DIFFRACTIONr_nbtor_other0.0870.22429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2310
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7921.53144
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00823990
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.83331625
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5674.51270
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1468medium positional0.140.5
2B1468medium positional0.140.5
1A2121loose positional0.545
2B2121loose positional0.545
1A1468medium thermal0.52
2B1468medium thermal0.52
1A2121loose thermal0.9210
2B2121loose thermal0.9210
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 79
Rwork0.152 1501
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)
10.6075-0.3538-0.2490.89210.18741.228-0.0299-0.088-0.02070.1180.06390.030.04710.0171-0.034-0.07710.0033-0.0066-0.0590.0093-0.0563-0.0610.371-0.827
20.64080.3441-0.2130.8407-0.20531.167-0.01070.09-0.0122-0.11210.0346-0.06360.0486-0.0079-0.024-0.0850.0062-0.0009-0.0663-0.0018-0.04558.3460.332-35.263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 250
2X-RAY DIFFRACTION2B2 - 250

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