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- PDB-3sr7: Crystal structure of S. mutans isopentenyl pyrophosphate isomerase -

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Basic information

Entry
Database: PDB / ID: 3sr7
TitleCrystal structure of S. mutans isopentenyl pyrophosphate isomerase
ComponentsIsopentenyl-diphosphate delta-isomerase
KeywordsISOMERASE / isopentenyl pyrophosphate isomerase / Tim-barrel
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 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Isopentenyl-diphosphate delta-isomerase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.036 Å
AuthorsLiu, Y.H. / Fu, T.M. / Liu, X. / Su, X.D.
CitationJournal: To be Published
Title: Crystal structure of S. mutans isopentenyl pyrophosphate isomerase
Authors: Liu, Y.H. / Fu, T.M. / Liu, X. / Su, X.D.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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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)163,7305
Polymers163,6354
Non-polymers951
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-54 kcal/mol
Surface area42540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.690, 76.420, 92.530
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40908.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: fni, SMU_939 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DUI9, isopentenyl-diphosphate Delta-isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.83 Å3/Da / Density % sol: 32.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 5mM MgCl2, 5mM MnCl2, 5mM CaCl2, 0.1M Tris HCl pH 8.0, 5% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9761 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9761 Å / Relative weight: 1
ReflectionResolution: 2.036→45.27 Å / Num. all: 75654 / Num. obs: 74368 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.081 / Net I/σ(I): 10.6
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10734 / Rsym value: 0.63 / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.036→41.921 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 2006 2.7 %random
Rwork0.2353 ---
obs0.2367 74177 97.82 %-
all-75845 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.184 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.3213 Å20 Å2-0.5301 Å2
2--29.2222 Å20 Å2
3----10.9008 Å2
Refinement stepCycle: LAST / Resolution: 2.036→41.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8309 0 5 153 8467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088464
X-RAY DIFFRACTIONf_angle_d1.03511479
X-RAY DIFFRACTIONf_dihedral_angle_d14.4333029
X-RAY DIFFRACTIONf_chiral_restr0.0711349
X-RAY DIFFRACTIONf_plane_restr0.0051465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.036-2.08690.39021410.38795068X-RAY DIFFRACTION97
2.0869-2.14340.43731460.34345105X-RAY DIFFRACTION97
2.1434-2.20640.37221270.30545110X-RAY DIFFRACTION97
2.2064-2.27760.33161620.28935060X-RAY DIFFRACTION97
2.2776-2.3590.31671310.26675140X-RAY DIFFRACTION98
2.359-2.45350.33561360.24865146X-RAY DIFFRACTION98
2.4535-2.56510.33071490.24125151X-RAY DIFFRACTION98
2.5651-2.70030.28411450.23345117X-RAY DIFFRACTION98
2.7003-2.86950.32161340.22645173X-RAY DIFFRACTION98
2.8695-3.0910.26011450.22975176X-RAY DIFFRACTION98
3.091-3.40190.30751480.23445187X-RAY DIFFRACTION98
3.4019-3.89390.26441460.22285215X-RAY DIFFRACTION99
3.8939-4.90470.23431480.19795212X-RAY DIFFRACTION99
4.9047-41.92940.26891480.22655311X-RAY DIFFRACTION98

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