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- PDB-7r7m: Crystal structure of Triosephosphate isomerase from Candidate div... -

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Basic information

Entry
Database: PDB / ID: 7r7m
TitleCrystal structure of Triosephosphate isomerase from Candidate division Katanobacteria (WWE3) bacterium
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / triosephosphate isomerase / glycolysis / gluconeogenesis
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function
Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciescandidate division WWE3 bacterium RAAC2_WWE3_1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVickers, C.J. / Patrick, W.M. / Fraga, D.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
Citation
Journal: To Be Published
Title: Structure of WweTPI - Candidate division WWE3
Authors: Vickers, C.J. / Patrick, W.M. / Fraga, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)47,6774
Polymers47,4872
Non-polymers1902
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-35 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.461, 39.499, 78.149
Angle α, β, γ (deg.)90.000, 103.333, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Triosephosphate isomerase


Mass: 23743.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) candidate division WWE3 bacterium RAAC2_WWE3_1 (bacteria)
Gene: DIU24_00595 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A656PMZ5, triose-phosphate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG pH 9.0, 25 % w/v PEG 1500.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2→43.69 Å / Num. obs: 26321 / % possible obs: 97.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.24 Å2 / CC1/2: 0.997 / Net I/σ(I): 24.3
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 15961 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yya

1yya


Resolution: 2→43.69 Å / SU ML: 0.1902 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 20.7624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2114 1270 4.87 %
Rwork0.1508 24791 -
obs0.1539 26061 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.05 Å2
Refinement stepCycle: LAST / Resolution: 2→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 10 476 3686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693270
X-RAY DIFFRACTIONf_angle_d0.81744449
X-RAY DIFFRACTIONf_chiral_restr0.0561519
X-RAY DIFFRACTIONf_plane_restr0.0049568
X-RAY DIFFRACTIONf_dihedral_angle_d5.9674451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.22971400.14932771X-RAY DIFFRACTION99.22
2.08-2.170.22681360.15642710X-RAY DIFFRACTION99.13
2.17-2.290.2131330.1492751X-RAY DIFFRACTION99.45
2.29-2.430.22481430.16352733X-RAY DIFFRACTION99.28
2.43-2.620.25581230.16472748X-RAY DIFFRACTION99.17
2.62-2.880.24011420.1692735X-RAY DIFFRACTION99.14
2.88-3.30.23191430.15932776X-RAY DIFFRACTION98.98
3.3-4.160.20681520.13312734X-RAY DIFFRACTION98.46
4.16-43.690.16081580.13972833X-RAY DIFFRACTION98.49

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