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- PDB-2zry: Crystal structure of Sulfolobus shibatae isopentenyl diphosphate ... -

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Basic information

Entry
Database: PDB / ID: 2zry
TitleCrystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and IPP.
ComponentsIsopentenyl-diphosphate delta-isomeraseIsopentenyl-diphosphate delta isomerase
KeywordsISOMERASE / type 2 / IDI / FMN / reduced form / IPP / isopentenyl diphosphate isomerase / Flavoprotein / Isoprene biosynthesis / NADP
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 / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesSulfolobus shibatae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.64 Å
AuthorsUnno, H. / Yamashita, S. / Ikeda, Y. / Sekiguchi, S. / Yoshida, N. / Yoshimura, T. / Kusunoki, M. / Nakayama, T. / Nishino, T. / Hemmi, H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.
Authors: Unno, H. / Yamashita, S. / Ikeda, Y. / Sekiguchi, S.Y. / Yoshida, N. / Yoshimura, T. / Kusunoki, M. / Nakayama, T. / Nishino, T. / Hemmi, H.
History
DepositionSep 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Mar 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 / 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 / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint-165 kcal/mol
Surface area45000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.359, 100.359, 334.607
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
13A
23B
33C
43D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARGAA3 - 3653 - 365
21ASPASPARGARGBB3 - 3653 - 365
31ASPASPARGARGCC3 - 3653 - 365
41ASPASPARGARGDD3 - 3653 - 365
12FNRFNRFNRFNRAE669
22FNRFNRFNRFNRBH669
32FNRFNRFNRFNRCK669
42FNRFNRFNRFNRDN669
13IPEIPEIPEIPEAF701
23IPEIPEIPEIPEBI701
33IPEIPEIPEIPECL701
43IPEIPEIPEIPEDO701

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Isopentenyl-diphosphate delta-isomerase / Isopentenyl-diphosphate delta isomerase / type 2 isopentenyl diphosphate 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-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl 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.: 404 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
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-17A / Wavelength: 1.0000, 1.13980, 1.14022, 1.04000
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 29, 2008 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.13981
31.140221
41.041
ReflectionResolution: 2.64→50 Å / Num. obs: 48278 / % possible obs: 93.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.9
Reflection shellResolution: 2.64→2.74 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.2 / % possible all: 68.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.64→49.63 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.606 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22254 2450 5.1 %RANDOM
Rwork0.18271 ---
obs0.18474 45809 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.393 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.64→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11232 0 184 404 11820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211613
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.98915660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82751452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1724.569464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.511152128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9011564
X-RAY DIFFRACTIONr_chiral_restr0.1230.21760
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028376
X-RAY DIFFRACTIONr_nbd_refined0.2160.26168
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2649
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.211
X-RAY DIFFRACTIONr_mcbond_it0.6971.57391
X-RAY DIFFRACTIONr_mcangle_it1.187211584
X-RAY DIFFRACTIONr_scbond_it1.8734723
X-RAY DIFFRACTIONr_scangle_it3.1384.54076
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2799tight positional0.050.05
12B2799tight positional0.050.05
13C2799tight positional0.060.05
14D2799tight positional0.050.05
21A31tight positional0.040.05
22B31tight positional0.040.05
23C31tight positional0.030.05
24D31tight positional0.040.05
31A14tight positional0.020.05
32B14tight positional0.040.05
33C14tight positional0.030.05
34D14tight positional0.040.05
11A2799tight thermal0.090.5
12B2799tight thermal0.090.5
13C2799tight thermal0.090.5
14D2799tight thermal0.090.5
21A31tight thermal0.090.5
22B31tight thermal0.120.5
23C31tight thermal0.10.5
24D31tight thermal0.140.5
31A14tight thermal0.090.5
32B14tight thermal0.110.5
33C14tight thermal0.090.5
34D14tight thermal0.090.5
LS refinement shellResolution: 2.637→2.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 123 -
Rwork0.245 2207 -
obs--62.52 %

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