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- PDB-4y96: Crystal structure of Triosephosphate Isomerase from Gemmata obscu... -

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Basic information

Entry
Database: PDB / ID: 4y96
TitleCrystal structure of Triosephosphate Isomerase from Gemmata obscuriglobus
ComponentsTriosephosphate Isomerase
KeywordsISOMERASE / TIM Barrel / TPI
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
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
PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesGemmata obscuriglobus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.581 Å
AuthorsRomero-Romero, S. / Rodriguez-Romero, A. / Fernandez-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 17, 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 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4138
Polymers54,1142
Non-polymers2996
Water11,512639
1
A: Triosephosphate Isomerase
hetero molecules

A: Triosephosphate Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,47610
Polymers54,1142
Non-polymers3628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4310 Å2
ΔGint-97 kcal/mol
Surface area18520 Å2
MethodPISA
2
B: Triosephosphate Isomerase
hetero molecules

B: Triosephosphate Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3506
Polymers54,1142
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area3920 Å2
ΔGint-69 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.778, 124.778, 134.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-449-

HOH

31A-467-

HOH

41A-691-

HOH

51B-447-

HOH

61B-449-

HOH

71B-455-

HOH

81B-468-

HOH

91B-475-

HOH

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Components

#1: Protein Triosephosphate Isomerase /


Mass: 27056.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Expression tag: GSH / Source: (gene. exp.) Gemmata obscuriglobus (bacteria) / Strain: UQM 2246 / Gene: tim / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: A0A0M3KL18*PLUS, triose-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M potassium sodium tartrate, 0.1 M sodium citrate tribasic pH 5.6, 2 M ammonium sulfate

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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: Nov 13, 2014
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→36.36 Å / Num. obs: 81335 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 19.56 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 9 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.8 / % possible all: 99.3

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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: 1B9B

1b9b


Resolution: 1.581→36.36 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 4125 5.08 %
Rwork0.1772 --
obs0.1784 81277 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.581→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 14 639 4385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063869
X-RAY DIFFRACTIONf_angle_d1.1385266
X-RAY DIFFRACTIONf_dihedral_angle_d12.6981410
X-RAY DIFFRACTIONf_chiral_restr0.042609
X-RAY DIFFRACTIONf_plane_restr0.005680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.581-1.59930.25041090.23052693X-RAY DIFFRACTION98
1.5993-1.61880.2671450.21982703X-RAY DIFFRACTION99
1.6188-1.63930.26621440.21692671X-RAY DIFFRACTION99
1.6393-1.66090.22391560.21042671X-RAY DIFFRACTION99
1.6609-1.68360.23491500.19952711X-RAY DIFFRACTION99
1.6836-1.70770.26691230.2042725X-RAY DIFFRACTION99
1.7077-1.73310.22171660.20062650X-RAY DIFFRACTION99
1.7331-1.76020.25161290.20272717X-RAY DIFFRACTION99
1.7602-1.78910.23271570.20212660X-RAY DIFFRACTION99
1.7891-1.81990.20481540.19282674X-RAY DIFFRACTION99
1.8199-1.8530.24721390.19542684X-RAY DIFFRACTION98
1.853-1.88870.23061460.19212695X-RAY DIFFRACTION98
1.8887-1.92720.24691140.1922696X-RAY DIFFRACTION98
1.9272-1.96910.19841610.18972665X-RAY DIFFRACTION98
1.9691-2.01490.18621530.18782662X-RAY DIFFRACTION98
2.0149-2.06530.21651460.18032639X-RAY DIFFRACTION97
2.0653-2.12110.20181420.18072674X-RAY DIFFRACTION97
2.1211-2.18360.18021320.18192690X-RAY DIFFRACTION97
2.1836-2.2540.18491470.17332635X-RAY DIFFRACTION96
2.254-2.33460.21091330.18362649X-RAY DIFFRACTION96
2.3346-2.4280.19511540.17472639X-RAY DIFFRACTION96
2.428-2.53850.23151550.18492620X-RAY DIFFRACTION95
2.5385-2.67230.20011360.17682632X-RAY DIFFRACTION95
2.6723-2.83970.21491330.19042633X-RAY DIFFRACTION94
2.8397-3.05880.19771540.16962605X-RAY DIFFRACTION94
3.0588-3.36640.20041360.17282611X-RAY DIFFRACTION93
3.3664-3.85310.14411420.15232596X-RAY DIFFRACTION92
3.8531-4.85270.16631400.14322597X-RAY DIFFRACTION90
4.8527-36.36930.24411290.18522655X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 74.4248 Å / Origin y: -14.3477 Å / Origin z: 2.1757 Å
111213212223313233
T0.1603 Å2-0.0091 Å2-0.0158 Å2-0.1027 Å20.0107 Å2--0.1404 Å2
L0.1522 °20.0052 °2-0.0932 °2-0.3104 °2-0.052 °2--0.2552 °2
S0.0331 Å °0.0195 Å °-0.0745 Å °0.0647 Å °-0.1104 Å °-0.0485 Å °0.0632 Å °-0.0254 Å °-0.104 Å °
Refinement TLS groupSelection details: all

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