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- PDB-3hyq: Crystal Structure of Isopentenyl-Diphosphate delta-Isomerase from... -

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Basic information

Entry
Database: PDB / ID: 3hyq
TitleCrystal Structure of Isopentenyl-Diphosphate delta-Isomerase from Salmonella entericase
ComponentsIsopentenyl-diphosphate Delta-isomeraseIsopentenyl-diphosphate delta isomerase
KeywordsISOMERASE / alpha-beta structure / Isoprene biosynthesis / Magnesium / Manganese / Metal-binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


isopentenyl-diphosphate Delta-isomerase / isopentenyl-diphosphate delta-isomerase activity / dimethylallyl diphosphate biosynthetic process / isoprenoid biosynthetic process / hydrolase activity / metal 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 speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.525 Å
AuthorsKim, Y. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Isopentenyl-Diphosphate delta-Isomerase from Salmonella entericase
Authors: Kim, Y. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isopentenyl-diphosphate Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)21,2621
Polymers21,2621
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Isopentenyl-diphosphate Delta-isomerase

A: Isopentenyl-diphosphate Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)42,5252
Polymers42,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1460 Å2
ΔGint-12 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.443, 64.152, 35.187
Angle α, β, γ (deg.)90.00, 101.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21A-408-

HOH

Detailsmonomer

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Components

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


Mass: 21262.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: idi / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q8ZM82, isopentenyl-diphosphate Delta-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.4 M ammonium dihydrogen phosphate, chymotripsyn (1:100), VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 31, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. all: 26450 / Num. obs: 26450 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 21.74 Å2 / Rsym value: 0.062 / Net I/σ(I): 19
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1015 / Rsym value: 0.308 / % possible all: 78

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX1.4_58refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.525→25.005 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1329 5.03 %RANDOM
Rwork0.163 ---
all0.164 26437 --
obs0.164 26437 97.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.683 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.775 Å2-0 Å21.2287 Å2
2---4.3546 Å2-0 Å2
3---1.5796 Å2
Refinement stepCycle: LAST / Resolution: 1.525→25.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 0 227 1455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.018
X-RAY DIFFRACTIONf_angle_deg1.536
X-RAY DIFFRACTIONf_dihedral_angle_d17.83
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.5249-1.58590.25411250.22752295242082
1.5859-1.65810.22461390.20032827296699
1.6581-1.74550.19971490.17228352984100
1.7455-1.85480.1961410.168128863027100
1.8548-1.9980.20651470.165428322979100
1.998-2.19890.21151560.159628493005100
2.1989-2.51690.17851500.161628633013100
2.5169-3.170.16551530.151628683021100
3.17-25.00860.17851690.15452853302299

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