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

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Basic information

Entry
Database: PDB / ID: 5css
TitleCrystal structure of triosephosphate isomerase from Thermoplasma acidophilum with glycerol 3-phosphate
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triosephosphate isomerase / Thermoplasma acidophilum / TIM / TPI / Glycerol 3-phosphate
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
SN-GLYCEROL-3-PHOSPHATE / Triosephosphate isomerase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsPark, S.H. / Kim, H.S. / Song, M.K. / Kim, K.R. / Park, J.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 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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.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 1.3Nov 6, 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)101,61412
Polymers100,7834
Non-polymers8308
Water7,224401
1
A: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8076
Polymers50,3922
Non-polymers4154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-56 kcal/mol
Surface area17470 Å2
MethodPISA
2
B: Triosephosphate isomerase
C: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8076
Polymers50,3922
Non-polymers4154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-56 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.633, 84.079, 143.539
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 / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 214 / Label seq-ID: 3 - 216

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

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-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.6 M sodium chloride, 9% PEG 6000, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 47245 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 20.9

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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: 5CSR

5csr


Resolution: 2.17→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.058 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 2391 5.1 %RANDOM
Rwork0.18308 ---
obs0.18516 44788 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.162 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å2-0 Å2
2--0.78 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.17→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 44 401 7085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196797
X-RAY DIFFRACTIONr_bond_other_d0.0070.026604
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9869174
X-RAY DIFFRACTIONr_angle_other_deg1.425315252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6385852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33523.803284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.843151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5411544
X-RAY DIFFRACTIONr_chiral_restr0.0810.21044
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217528
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021452
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_it2.8493.0913420
X-RAY DIFFRACTIONr_mcbond_other2.8483.093419
X-RAY DIFFRACTIONr_mcangle_it4.244.624268
X-RAY DIFFRACTIONr_mcangle_other4.244.6214269
X-RAY DIFFRACTIONr_scbond_it4.1523.6333377
X-RAY DIFFRACTIONr_scbond_other4.1523.6333377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5485.2084907
X-RAY DIFFRACTIONr_long_range_B_refined8.56425.3477793
X-RAY DIFFRACTIONr_long_range_B_other8.56425.2427673
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)
11A133180.07
12B133180.07
21A130700.09
22C130700.09
31A131280.08
32D131280.08
41B130990.08
42C130990.08
51B131700.08
52D131700.08
61C131990.07
62D131990.07
LS refinement shellResolution: 2.169→2.225 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 191 -
Rwork0.253 3118 -
obs--96.3 %

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