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- PDB-1vcg: Crystal Structure of IPP isomerase at P43212 -

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Basic information

Entry
Database: PDB / ID: 1vcg
TitleCrystal Structure of IPP isomerase at P43212
Componentsisopentenyl-diphosphate delta-isomerase
KeywordsISOMERASE / TIM barrel / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsWada, T. / Park, S.-Y. / Tame, R.H. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of IPP isomerase at P43212
Authors: Wada, T. / Park, S.-Y. / Tame, R.H. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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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)147,2188
Polymers145,3934
Non-polymers1,8254
Water00
1
A: isopentenyl-diphosphate delta-isomerase
B: isopentenyl-diphosphate delta-isomerase
C: isopentenyl-diphosphate delta-isomerase
D: isopentenyl-diphosphate delta-isomerase
hetero molecules

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)294,43716
Polymers290,7868
Non-polymers3,6518
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-81 kcal/mol
Surface area44290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.953, 112.953, 261.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a octamer generated from the tetramer in the asymmetric unit by the operation: y, x, -z.

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Components

#1: Protein
isopentenyl-diphosphate delta-isomerase


Mass: 36348.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q746I8, isopentenyl-diphosphate Delta-isomerase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 3.08 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, sodium chloride, MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9803 Å / Relative weight: 1
ReflectionResolution: 3.01→20 Å / Num. obs: 32106 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.05 / Net I/σ(I): 24.1
Reflection shellResolution: 3.01→3.12 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 2217 / Rsym value: 0.198 / % possible all: 65.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.02→19.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 254990.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1593 5 %RANDOM
Rwork0.24 ---
obs0.24 32077 94.3 %-
all-32106 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.6711 Å2 / ksol: 0.314154 e/Å3
Displacement parametersBiso mean: 54.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2---2.04 Å20 Å2
3---4.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.02→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9553 0 124 0 9677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.632.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.02→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 217 5.5 %
Rwork0.339 3731 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FMN.PARAMFMN.TOP

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