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- PDB-4y90: Crystal structure of Triosephosphate Isomerase from Deinococcus r... -

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Basic information

Entry
Database: PDB / ID: 4y90
TitleCrystal structure of Triosephosphate Isomerase from Deinococcus radiodurans
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM Barrel / TPI
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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 speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRomero-Romero, S. / Rodriguez-Romero, A. / Fernadez-Velasco, D.A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia de Mexico166472 Mexico
Consejo Nacional de Ciencia y Tecnologia de Mexico99857 Mexico
CitationJournal: Phys Chem Chem Phys / Year: 2015
Title: Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins.
Authors: Romero-Romero, S. / Costas, M. / Rodriguez-Romero, A. / Alejandro Fernandez-Velasco, D.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Data collection
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,05426
Polymers102,4754
Non-polymers1,57922
Water14,988832
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,19914
Polymers51,2382
Non-polymers96112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-104 kcal/mol
Surface area18160 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,85512
Polymers51,2382
Non-polymers61810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-124 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.620, 169.620, 202.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11D-420-

HOH

21D-448-

HOH

DetailsDimer by Gel Filtration

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 25618.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expression tag: GSH
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: DSM 20539 / JCM 16871 / Gene: tpiA, DR_1339 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RUP5, triose-phosphate isomerase

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Non-polymers , 5 types, 854 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.8 M ammonium sulfate, 0.1 M sodium citrate tribasic pH 5.6, 0.2 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 4, 2013
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→36.133 Å / Num. obs: 64962 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
CrystalCleardata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YYA

1yya


Resolution: 2.1→36.133 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 3285 5.06 %
Rwork0.1357 --
obs0.1382 64947 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 87 832 8027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117318
X-RAY DIFFRACTIONf_angle_d1.2969948
X-RAY DIFFRACTIONf_dihedral_angle_d12.7372649
X-RAY DIFFRACTIONf_chiral_restr0.051143
X-RAY DIFFRACTIONf_plane_restr0.0061318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13070.24051220.17382575X-RAY DIFFRACTION95
2.1307-2.1640.20661570.16532644X-RAY DIFFRACTION100
2.164-2.19950.21421650.15852658X-RAY DIFFRACTION100
2.1995-2.23740.2171300.14712666X-RAY DIFFRACTION100
2.2374-2.27810.24631480.15222665X-RAY DIFFRACTION100
2.2781-2.32190.20161340.14782691X-RAY DIFFRACTION100
2.3219-2.36930.21091190.14522671X-RAY DIFFRACTION100
2.3693-2.42080.19261340.14432681X-RAY DIFFRACTION100
2.4208-2.47710.24571430.14492689X-RAY DIFFRACTION100
2.4771-2.5390.19081360.13632667X-RAY DIFFRACTION100
2.539-2.60760.19281400.13642687X-RAY DIFFRACTION100
2.6076-2.68430.18771680.14132647X-RAY DIFFRACTION100
2.6843-2.7710.21711460.14532678X-RAY DIFFRACTION100
2.771-2.870.2531420.15162680X-RAY DIFFRACTION100
2.87-2.98480.20331570.15312667X-RAY DIFFRACTION100
2.9848-3.12060.20441340.14992684X-RAY DIFFRACTION100
3.1206-3.2850.19881380.13322694X-RAY DIFFRACTION100
3.285-3.49070.17111580.12682698X-RAY DIFFRACTION100
3.4907-3.75990.14861310.11412708X-RAY DIFFRACTION100
3.7599-4.13780.15751470.11042711X-RAY DIFFRACTION100
4.1378-4.73540.13751530.10372697X-RAY DIFFRACTION100
4.7354-5.96180.16011510.13172722X-RAY DIFFRACTION99
5.9618-36.13840.16371320.14962782X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -42.3282 Å / Origin y: 122.2282 Å / Origin z: 218.2869 Å
111213212223313233
T0.0797 Å20.0067 Å2-0.0015 Å2-0.1193 Å2-0.0178 Å2--0.0951 Å2
L0.0873 °2-0.0749 °2-0.1155 °2-0.0234 °20.0163 °2--0.019 °2
S0.0411 Å °-0.0129 Å °0.0054 Å °-0.0143 Å °-0.0305 Å °0.0054 Å °-0.0089 Å °-0.0035 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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