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- PDB-3dh7: Structure of T. thermophilus IDI-2 in complex with PPi -

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Basic information

Entry
Database: PDB / ID: 3dh7
TitleStructure of T. thermophilus IDI-2 in complex with PPi
ComponentsIsopentenyl-diphosphate delta-isomerase
KeywordsISOMERASE / IDI / complex / Plasmid
Function / homology
Function and homology information


isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / isoprenoid biosynthetic process / NADPH binding / FMN binding / oxidoreductase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Isopentenyl-diphosphate delta-isomerase, FMN-dependent / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PYROPHOSPHATE 2- / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
Authorsde Ruyck, J. / Wouters, J.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate
Authors: de Ruyck, J. / Pouyez, J. / Rothman, S.C. / Poulter, D. / Wouters, J.
History
DepositionJun 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isopentenyl-diphosphate delta-isomerase
B: Isopentenyl-diphosphate delta-isomerase
C: Isopentenyl-diphosphate delta-isomerase
D: Isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,44510
Polymers144,2674
Non-polymers2,1776
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-75.2 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.528, 142.528, 109.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Isopentenyl-diphosphate delta-isomerase


Mass: 36066.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHB110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53W52
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 4.46 Å3/Da / Density % sol: 72.41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5 / Details: pH5.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.97→20 Å / Num. obs: 49971

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.97→19.92 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.756 / SU B: 14.974 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29254 2538 5.1 %RANDOM
Rwork0.21092 ---
obs0.21508 47599 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.776 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.97→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9620 0 142 229 9991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0229918
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0982.01913461
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.67451255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26722.03404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.119151666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.89415118
X-RAY DIFFRACTIONr_chiral_restr0.1990.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027388
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3190.26682
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3510.26649
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2644
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2121.56445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.03229918
X-RAY DIFFRACTIONr_scbond_it3.08834208
X-RAY DIFFRACTIONr_scangle_it5.5954.53543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.971→3.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 145 -
Rwork0.28 2542 -
obs--72.31 %

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