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- PDB-1hzt: CRYSTAL STRUCTURE OF METAL-FREE ISOPENTENYL DIPHOSPHATE:DIMETHYLA... -

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Basic information

Entry
Database: PDB / ID: 1hzt
TitleCRYSTAL STRUCTURE OF METAL-FREE ISOPENTENYL DIPHOSPHATE:DIMETHYLALLYL DIPHOSPHATE ISOMERASE
ComponentsISOPENTENYL DIPHOSPHATE DELTA-ISOMERASE
KeywordsISOMERASE / isopentenyl / dimethylallyl / isoprenoids
Function / homology
Function and homology information


isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / dimethylallyl diphosphate biosynthetic process / isoprenoid biosynthetic process / DNA damage response / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
Isopentenyl-diphosphate delta-isomerase, type 1 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Isopentenyl-diphosphate Delta-isomerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.45 Å
AuthorsDurbecq, V. / Sainz, G. / Oudjama, Y. / Clantin, B. / Bompard-Gilles, C. / Tricot, C. / Caillet, J. / Stalon, V. / Droogmans, L. / Villeret, V.
CitationJournal: Embo J. / Year: 2001
Title: Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.
Authors: Durbecq, V. / Sainz, G. / Oudjama, Y. / Clantin, B. / Bompard-Gilles, C. / Tricot, C. / Caillet, J. / Stalon, V. / Droogmans, L. / Villeret, V.
History
DepositionJan 26, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ISOPENTENYL DIPHOSPHATE DELTA-ISOMERASE


Theoretical massNumber of molelcules
Total (without water)21,6021
Polymers21,6021
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.400, 71.400, 61.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ISOPENTENYL DIPHOSPHATE DELTA-ISOMERASE / DIMETHYLALLYL DIPHOSPHATE ISOMERASE


Mass: 21602.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: IDI / Plasmid: PYL20 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q46822, isopentenyl-diphosphate Delta-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG2000 monomethylether, Tris, maleate, ammonium sulfate, glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Oudjama, Y., (2001) Acta Crystallogr., 57, 287.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
210 %(w/v)PEG2000 MME1reservoir
3100 mMTris-maleate1reservoir
4100 mMammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.97858, 0.97873
SYNCHROTRONESRF ID14-220.9326
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 1, 2000
ADSC QUANTUM 42CCDJan 1, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978581
20.978731
30.93261
ReflectionBiso Wilson estimate: 20.1 Å2

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Processing

Software
NameVersionClassification
SOLVEphasing
MLPHAREphasing
WARPmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.45→23.37 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1072282.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1617 5.1 %RANDOM
Rwork0.192 ---
obs0.192 31943 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 86.9 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20.98 Å20 Å2
2--1.98 Å20 Å2
3----3.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.45→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 0 165 1388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 274 5.2 %
Rwork0.269 5001 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64
LS refinement shell
*PLUS
Rfactor Rfree: 0.267 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.269

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