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- PDB-5csr: Crystal structure of triosephosphate isomerase from Thermoplasma ... -

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Basic information

Entry
Database: PDB / ID: 5csr
TitleCrystal structure of triosephosphate isomerase from Thermoplasma acidophilium
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triosephoshate isomerase / Thermoplasma acidophilium / TIM / TPI
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function
Triosephosphate isomerase, archaeal / 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 speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPark, S.H. / Kim, H.S. / Song, M.K. / Park, H.S. / Han, B.W.
CitationJournal: Plos One / Year: 2015
Title: Structure and Stability of the Dimeric Triosephosphate Isomerase from the Thermophilic Archaeon Thermoplasma acidophilum.
Authors: Park, S.H. / Kim, H.S. / Park, M.S. / Moon, S. / Song, M.K. / Park, H.S. / Hahn, H. / Kim, S.J. / Bae, E. / Kim, H.J. / Han, B.W.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,29412
Polymers100,7834
Non-polymers5108
Water10,106561
1
A: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6476
Polymers50,3922
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-45 kcal/mol
Surface area19370 Å2
MethodPISA
2
B: Triosephosphate isomerase
C: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6476
Polymers50,3922
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-45 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.486, 113.963, 114.796
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA1 - 2153 - 217
21LEULEUBB1 - 2153 - 217
12GLUGLUAA1 - 2143 - 216
22GLUGLUCC1 - 2143 - 216
13GLUGLUAA1 - 2143 - 216
23GLUGLUDD1 - 2143 - 216
14GLUGLUBB1 - 2143 - 216
24GLUGLUCC1 - 2143 - 216
15GLUGLUBB1 - 2143 - 216
25GLUGLUDD1 - 2143 - 216
16HISHISCC1 - 2203 - 222
26HISHISDD1 - 2203 - 222

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 25195.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: tpiA, Ta0313 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HLB6, triose-phosphate isomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 M sodium chloride, 10% PEG 6000, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 73921 / % possible obs: 99 % / Redundancy: 7.1 % / Net I/σ(I): 32.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HG3

1hg3


Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.419 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21541 3707 5 %RANDOM
Rwork0.18014 ---
obs0.18191 70068 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å2-0 Å20 Å2
2---0.31 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6764 0 28 561 7353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196944
X-RAY DIFFRACTIONr_bond_other_d0.0080.026768
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9819372
X-RAY DIFFRACTIONr_angle_other_deg1.389315626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87523.878294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.966151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6711544
X-RAY DIFFRACTIONr_chiral_restr0.1030.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217738
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021498
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_it2.7182.9823496
X-RAY DIFFRACTIONr_mcbond_other2.7192.9813495
X-RAY DIFFRACTIONr_mcangle_it3.7544.4474370
X-RAY DIFFRACTIONr_mcangle_other3.7544.4484371
X-RAY DIFFRACTIONr_scbond_it3.9943.493448
X-RAY DIFFRACTIONr_scbond_other3.9943.493448
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1425.0245003
X-RAY DIFFRACTIONr_long_range_B_refined7.95424.137347
X-RAY DIFFRACTIONr_long_range_B_other7.78523.7377145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128060.06
12B128060.06
21A119660.12
22C119660.12
31A119630.12
32D119630.12
41B119800.12
42C119800.12
51B119170.12
52D119170.12
61C130140.05
62D130140.05
LS refinement shellResolution: 1.939→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 275 -
Rwork0.261 5056 -
obs--98.63 %

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