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- PDB-2h6r: Crystal Structure of triosephosphate isomerase (TIM) from Methano... -

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Basic information

Entry
Database: PDB / ID: 2h6r
TitleCrystal Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / beta-alpha barrel
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytosol
Similarity search - Function
Triosephosphate isomerase, archaeal / 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, archaeal / 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 speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Balaram, H. / Balaram, P. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of triosephosphate isomerase (TIM) from Methanocaldococcus jannaschii
Authors: Gayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Azeez, S. / Balaram, H. / Balaram, P. / Murthy, M.R.N.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 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
C: Triosephosphate isomerase
D: Triosephosphate isomerase
E: Triosephosphate isomerase
F: Triosephosphate isomerase
G: Triosephosphate isomerase
H: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)186,1768
Polymers186,1768
Non-polymers00
Water6,918384
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
C: Triosephosphate isomerase
D: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)93,0884
Polymers93,0884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-53 kcal/mol
Surface area31260 Å2
MethodPISA
2
E: Triosephosphate isomerase
F: Triosephosphate isomerase
G: Triosephosphate isomerase
H: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)93,0884
Polymers93,0884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-52 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.340, 139.340, 80.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 23271.996 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: TPIA / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 / References: UniProt: Q58923, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8
Details: 30% PEG 3350, 0.2M Magnesium chloride, 0.1M Tris pH 8.0, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAC Science DIP-2040 / Detector: IMAGE PLATE / Date: Mar 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
tetartohedral11h,k,l10.25
tetartohedral11k,h,-l20.25
tetartohedral11-k,-h,-l30.25
tetartohedral11-h,-k,l40.25
ReflectionResolution: 2.3→50 Å / Num. all: 76266 / Num. obs: 76266 / % possible obs: 96.3 % / Redundancy: 14.26 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 20.15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 6.3 / Num. unique all: 7537

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HG3

1hg3


Resolution: 2.3→34.28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 80028.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined using modified CNS files for tetartohedral twinning (Barends, et al., 2005, Acta Cryst D61, 613-621). The crystal structure has been determined from a ...Details: The structure was refined using modified CNS files for tetartohedral twinning (Barends, et al., 2005, Acta Cryst D61, 613-621). The crystal structure has been determined from a tetartohedrally twinned crystal. The twinning operator are (h,k,l)(k,h,-l)(-k,-h,-l)(-h,-k,l) and the twinning fraction are 0.25, 0.25, 0.25, 0.25.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3415 4.5 %RANDOM
Rwork0.213 ---
obs0.213 72282 92.7 %-
all-78046 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1616 Å2 / ksol: 0.364509 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.179 Å2-1.705 Å20 Å2
2--1.528 Å20 Å2
3----1.707 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12038 0 0 384 12422
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.324 355 4.2 %
Rwork0.299 7958 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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