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- PDB-1p0n: IPP:DMAPP isomerase type II, FMN complex -

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Basic information

Entry
Database: PDB / ID: 1p0n
TitleIPP:DMAPP isomerase type II, FMN complex
ComponentsIsopentenyl-diphosphate delta-isomerase
KeywordsISOMERASE / terpene biosynthesis / isopentenyl diphosphate / dimethylallyl diphosphate / flavoprotein
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 / IMP dehydrogenase / GMP reductase domain / 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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsSteinbacher, S. / Kaiser, J. / Gerhardt, S. / Eisenreich, W. / Huber, R. / Bacher, A. / Rohdich, F.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Type II Isopentenyl Diphosphate:Dimethylallyl Diphosphate Isomerase from Bacillus subtilis
Authors: Steinbacher, S. / Kaiser, J. / Gerhardt, S. / Eisenreich, W. / Huber, R. / Bacher, A. / Rohdich, F.
History
DepositionApr 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,4384
Polymers74,5252
Non-polymers9132
Water00
1
A: Isopentenyl-diphosphate delta-isomerase
B: Isopentenyl-diphosphate delta-isomerase
hetero molecules

A: Isopentenyl-diphosphate delta-isomerase
B: Isopentenyl-diphosphate delta-isomerase
hetero molecules

A: Isopentenyl-diphosphate delta-isomerase
B: Isopentenyl-diphosphate delta-isomerase
hetero molecules

A: Isopentenyl-diphosphate delta-isomerase
B: Isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,75116
Polymers298,1008
Non-polymers3,6518
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30640 Å2
ΔGint-241 kcal/mol
Surface area85540 Å2
MethodPISA
2
A: Isopentenyl-diphosphate delta-isomerase
hetero molecules

A: Isopentenyl-diphosphate delta-isomerase
hetero molecules

A: Isopentenyl-diphosphate delta-isomerase
hetero molecules

A: Isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,8758
Polymers149,0504
Non-polymers1,8254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
3
B: Isopentenyl-diphosphate delta-isomerase
hetero molecules

B: Isopentenyl-diphosphate delta-isomerase
hetero molecules

B: Isopentenyl-diphosphate delta-isomerase
hetero molecules

B: Isopentenyl-diphosphate delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,8758
Polymers149,0504
Non-polymers1,8254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.027, 115.027, 139.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Isopentenyl-diphosphate delta-isomerase / IPP:DMAPP isomerase type II


Mass: 37262.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: P50740, isopentenyl-diphosphate Delta-isomerase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / 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: 3.61 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: PEG 400, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
250 mMTris-HCl1drop
30.02 %(w/v)1droppH8.0NaN3
470 mMtricine1reservoir
530 mMTris-HCl1reservoir
6170 mM1reservoirNaCl
714 %(v/v)PEG4001reservoir
82.5 %(w/v)PEG80001reservoirpH8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 5, 2002 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 22127 / Num. obs: 22127 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.37 / % possible all: 97.3
Reflection
*PLUS
Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.37

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1P0K

1p0k


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The bond distance of SD-CE in MET B 156 is slightly long
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 1077 -random
Rwork0.2193 ---
all0.2211 22099 --
obs0.2211 22099 98.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.381 Å20 Å20 Å2
2--4.381 Å20 Å2
3----8.762 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 62 0 4579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010223
X-RAY DIFFRACTIONc_angle_deg1.28762
Refinement
*PLUS
Rfactor Rfree: 0.256 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.29

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