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- PDB-3b06: Crystal structure of Sulfolobus shibatae isopentenyl diphosphate ... -

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Basic information

Entry
Database: PDB / ID: 3b06
TitleCrystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and DMAPP.
ComponentsIsopentenyl-diphosphate delta-isomeraseIsopentenyl-diphosphate delta isomerase
KeywordsISOMERASE / TYPE 2 / IDI / FMN / ISOPENTENYL DIPHOSPHATE ISOMERASE / DMAPP
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
DIMETHYLALLYL DIPHOSPHATE / Chem-FNR / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesSulfolobus shibatae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsUnno, H. / Nagai, T. / Hemmi, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.
Authors: Nagai, T. / Unno, H. / Janczak, M.W. / Yoshimura, T. / Poulter, C.D. / Hemmi, H.
History
DepositionJun 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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)164,81816
Polymers161,9034
Non-polymers2,91512
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-105 kcal/mol
Surface area46880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.842, 100.842, 334.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 2 / Auth seq-ID: 10 - 360 / Label seq-ID: 10 - 360

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Isopentenyl-diphosphate delta-isomerase / Isopentenyl-diphosphate delta isomerase / IPP isomerase / Isopentenyl pyrophosphate isomerase


Mass: 40475.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: fni, idi / Plasmid: PET-15B / Production host: Escherichia coli (E. coli)
References: UniProt: P61615, isopentenyl-diphosphate Delta-isomerase
#2: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical
ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 30% PEG 400, 0.2M SODIUM CITRATE, 0.1M TRIS-HCL, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 73441 / % possible obs: 93.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 22.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 5.7 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→37.39 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.873 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23883 3699 5.1 %RANDOM
Rwork0.20416 ---
obs0.20595 69424 93.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.232 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.29→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11232 0 184 294 11710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02211604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.98915660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16551452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30524.569464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.855152128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0311564
X-RAY DIFFRACTIONr_chiral_restr0.1730.21760
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218396
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621.57200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85211584
X-RAY DIFFRACTIONr_scbond_it3.12834404
X-RAY DIFFRACTIONr_scangle_it5.2124.54076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1404tight positional0.060.05
B1404tight positional0.060.05
C1404tight positional0.060.05
D1404tight positional0.050.05
A1289medium positional0.080.5
B1289medium positional0.080.5
C1289medium positional0.090.5
D1289medium positional0.070.5
A1404tight thermal0.230.5
B1404tight thermal0.240.5
C1404tight thermal0.240.5
D1404tight thermal0.220.5
A1289medium thermal0.232
B1289medium thermal0.242
C1289medium thermal0.242
D1289medium thermal0.232
LS refinement shellResolution: 2.295→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 291 -
Rwork0.243 5159 -
obs--96.73 %

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