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- PDB-4s3f: IspG in complex with Inhibitor 8 (compound 1077) -

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Basic information

Entry
Database: PDB / ID: 4s3f
TitleIspG in complex with Inhibitor 8 (compound 1077)
Components4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
KeywordsOXIDOREDUCTASE / Methylerythritol-Phosphate Pathway / Terpene Biosynthesis / Iron-Sulfur Enzymes / Reaction Mechanisms / Drug Development
Function / homology
Function and homology information


(E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (flavodoxin) / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) / 4-hydroxy-3-methylbut-2-enyl-diphosphate synthase activity (flavodoxin) / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial / GcpE protein / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel ...4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial / GcpE protein / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
but-3-yn-1-yl trihydrogen diphosphate / FE3-S4 CLUSTER / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsQuitterer, F. / Frank, A. / Wang, K. / Rao, G. / O'Dowd, B. / Li, J. / Guerra, F. / Abdel-Azeim, S. / Bacher, A. / Eppinger, J. ...Quitterer, F. / Frank, A. / Wang, K. / Rao, G. / O'Dowd, B. / Li, J. / Guerra, F. / Abdel-Azeim, S. / Bacher, A. / Eppinger, J. / Oldfield, E. / Groll, M.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE).
Authors: Quitterer, F. / Frank, A. / Wang, K. / Rao, G. / O'Dowd, B. / Li, J. / Guerra, F. / Abdel-Azeim, S. / Bacher, A. / Eppinger, J. / Oldfield, E. / Groll, M.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8043
Polymers44,2781
Non-polymers5262
Water4,179232
1
A: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules

A: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6086
Polymers88,5562
Non-polymers1,0524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7240 Å2
ΔGint-78 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.370, 62.340, 86.370
Angle α, β, γ (deg.)90.00, 127.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1175-

HOH

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Components

#1: Protein 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase


Mass: 44278.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8/DSM 579 / Gene: ispG, TTHA0305 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLI8, EC: 1.17.7.1
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-43W / but-3-yn-1-yl trihydrogen diphosphate


Mass: 230.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS PROPANE, 20% PEG3350, 0.2 M Na2SO4 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 52217 / Num. obs: 49188 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.6 / % possible all: 96.4

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S38

4s38


Resolution: 1.7→10 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.883 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 2460 5 %RANDOM
Rwork0.13153 ---
obs0.13388 46728 94.57 %-
all-49188 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.988 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0 Å20.01 Å2
2---0.04 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 20 232 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193253
X-RAY DIFFRACTIONr_bond_other_d0.0010.023213
X-RAY DIFFRACTIONr_angle_refined_deg1.6912.0014424
X-RAY DIFFRACTIONr_angle_other_deg0.7737409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00722.707133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69915568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1051534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213668
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02688
X-RAY DIFFRACTIONr_mcbond_it3.212.4691655
X-RAY DIFFRACTIONr_mcbond_other3.22.4671654
X-RAY DIFFRACTIONr_mcangle_it3.9213.7162085
X-RAY DIFFRACTIONr_mcangle_other3.923.7182086
X-RAY DIFFRACTIONr_scbond_it5.1523.081598
X-RAY DIFFRACTIONr_scbond_other5.1633.0791590
X-RAY DIFFRACTIONr_scangle_other5.9594.3922324
X-RAY DIFFRACTIONr_long_range_B_refined5.92121.3043701
X-RAY DIFFRACTIONr_long_range_B_other5.73220.9333630
X-RAY DIFFRACTIONr_rigid_bond_restr3.65836466
X-RAY DIFFRACTIONr_sphericity_free32.345576
X-RAY DIFFRACTIONr_sphericity_bonded14.64256552
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 181 -
Rwork0.285 3430 -
obs--96.81 %
Refinement TLS params.Method: refined / Origin x: -12.7916 Å / Origin y: 23.2433 Å / Origin z: 2.8616 Å
111213212223313233
T0.0044 Å20.0007 Å20.0042 Å2-0.0108 Å20.0006 Å2--0.0094 Å2
L0.0911 °2-0.0163 °2-0.0091 °2-0.005 °2-0.003 °2--0.0927 °2
S0.0009 Å °-0.0043 Å °0.0003 Å °0.0017 Å °0.0007 Å °0.0041 Å °-0.0075 Å °-0.0118 Å °-0.0016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 404
2X-RAY DIFFRACTION1A901 - 902
3X-RAY DIFFRACTION1A1001 - 1232

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