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- PDB-1p0k: IPP:DMAPP isomerase type II apo structure -

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Basic information

Entry
Database: PDB / ID: 1p0k
TitleIPP:DMAPP isomerase type II apo structure
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
PHOSPHATE ION / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 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 1.3Mar 13, 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

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)74,7154
Polymers74,5252
Non-polymers1902
Water9,692538
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)298,86016
Polymers298,1008
Non-polymers7608
Water1448
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 area26330 Å2
ΔGint-244 kcal/mol
Surface area88240 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)149,4308
Polymers149,0504
Non-polymers3804
Water724
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)149,4308
Polymers149,0504
Non-polymers3804
Water724
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)115.833, 115.833, 141.520
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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 538 / 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: 3.33 Å3/Da / Density % sol: 62.76 %
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: Oct 12, 2002 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 72016 / Num. obs: 72016 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / % possible all: 100
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 100 % / Rmerge(I) obs: 0.47

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
CCP4model building
CNS1.1refinement
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→15 Å / Isotropic thermal model: isoptropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The bond dinstance of SD-CE in MET A 95 is slightly long
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 3646 -random
Rwork0.1991 ---
all0.2002 71797 --
obs0.2002 71797 98.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.822 Å20 Å20 Å2
2--2.822 Å20 Å2
3----5.643 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 10 538 5093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011313
X-RAY DIFFRACTIONc_angle_deg1.38744
Refinement
*PLUS
Rfactor Rfree: 0.221 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.39

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