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

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Basic information

Entry
Database: PDB / ID: 3vkj
TitleCrystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase, octameric form
ComponentsIsopentenyl-diphosphate delta-isomeraseIsopentenyl-diphosphate delta isomerase
KeywordsISOMERASE / type 2 isopentenyl diphosphate isomerase
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
Chem-FNR / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesSulfolobus shibatae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNakatani, H. / Goda, S. / Unno, H. / Nagai, T. / Yoshimura, T. / Hemmi, H.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Substrate-Induced Change in the Quaternary Structure of Type 2 Isopentenyl Diphosphate Isomerase from Sulfolobus shibatae.
Authors: Nakatani, H. / Goda, S. / Unno, H. / Nagai, T. / Yoshimura, T. / Hemmi, H.
History
DepositionNov 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
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

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)163,7378
Polymers161,9034
Non-polymers1,8334
Water13,043724
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)327,47316
Polymers323,8078
Non-polymers3,6678
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area37960 Å2
ΔGint-276 kcal/mol
Surface area90670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.841, 100.841, 336.651
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
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 365
2111B3 - 365
3111C3 - 365
4111D3 - 365
1124A669
2124B669
3124C669
4124D669

NCS ensembles :
ID
1
2

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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 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris-HCl, 0.2M sodium citrate, 30% PEG 400, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 180131 / % possible obs: 94.7 % / Redundancy: 8.5 %
Reflection shellResolution: 1.7→1.73 Å / % possible all: 77.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→35.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.689 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 9047 5 %RANDOM
Rwork0.185 ---
obs0.18644 170951 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.746 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11200 0 124 724 12048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.02211520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6281.98415540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07751448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91224.522460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.277152124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0461564
X-RAY DIFFRACTIONr_chiral_restr0.2510.21756
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218344
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_it1.3191.57180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.331211552
X-RAY DIFFRACTIONr_scbond_it3.64934340
X-RAY DIFFRACTIONr_scangle_it6.0334.53988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2791tight positional0.180.05
11B2791tight positional0.170.05
11C2791tight positional0.190.05
11D2791tight positional0.170.05
22A31medium positional0.040.5
22B31medium positional0.050.5
22C31medium positional0.050.5
22D31medium positional0.040.5
11A2791tight thermal0.580.5
11B2791tight thermal0.560.5
11C2791tight thermal0.670.5
11D2791tight thermal0.530.5
22A31medium thermal0.962
22B31medium thermal1.142
22C31medium thermal1.212
22D31medium thermal1.142
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 580 -
Rwork0.229 10030 -
obs--77.1 %

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