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- PDB-4s3c: IspG in complex with Epoxide Intermediate -

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Basic information

Entry
Database: PDB / ID: 4s3c
TitleIspG in complex with Epoxide Intermediate
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) / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 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 TIM-barrel domain / 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 TIM-barrel domain / 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
Chem-43Q / IRON/SULFUR 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: 1.45 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 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 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

Downloads & links

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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)45,0014
Polymers44,2781
Non-polymers7233
Water5,062281
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)90,0028
Polymers88,5562
Non-polymers1,4466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8150 Å2
ΔGint-64 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.930, 62.840, 86.200
Angle α, β, γ (deg.)90.00, 127.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1232-

HOH

21A-1237-

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-43Q / (3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium, carbokation intermediate


Mass: 279.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O9P2
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
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: X06SA / Wavelength: 0.971 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: 0.971 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 84126 / Num. obs: 81686 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.9
Reflection shellResolution: 1.45→1.55 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.4 / % possible all: 97.7

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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: 1.45→10 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.979 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16103 4085 5 %RANDOM
Rwork0.12305 ---
obs0.12498 77599 97.43 %-
all-81684 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.05 Å2
2--0.23 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 30 281 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193270
X-RAY DIFFRACTIONr_bond_other_d0.0010.023228
X-RAY DIFFRACTIONr_angle_refined_deg2.7782.0174491
X-RAY DIFFRACTIONr_angle_other_deg1.4853.0017440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7245421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6822.652132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.591534
X-RAY DIFFRACTIONr_chiral_restr0.2070.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213664
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0712.1141657
X-RAY DIFFRACTIONr_mcbond_other4.0342.1111656
X-RAY DIFFRACTIONr_mcangle_it4.7843.1842087
X-RAY DIFFRACTIONr_mcangle_other4.5723.1922088
X-RAY DIFFRACTIONr_scbond_it7.0112.7621613
X-RAY DIFFRACTIONr_scbond_other6.5682.7571613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3153.8852343
X-RAY DIFFRACTIONr_long_range_B_refined6.61718.8973791
X-RAY DIFFRACTIONr_long_range_B_other6.61718.8973791
X-RAY DIFFRACTIONr_rigid_bond_restr6.17636498
X-RAY DIFFRACTIONr_sphericity_free29.853579
X-RAY DIFFRACTIONr_sphericity_bonded17.89856620
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 299 -
Rwork0.248 5683 -
obs--98.52 %
Refinement TLS params.Method: refined / Origin x: -12.5907 Å / Origin y: 23.4218 Å / Origin z: 2.7327 Å
111213212223313233
T0.0037 Å20.0001 Å2-0.0006 Å2-0.024 Å2-0.0001 Å2--0.0111 Å2
L0.0104 °2-0.0018 °20.0021 °2-0.0015 °2-0.0006 °2--0.0046 °2
S-0.0001 Å °-0.0011 Å °-0 Å °0.0004 Å °0.0006 Å °0.0003 Å °-0.0005 Å °-0.0011 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 404
2X-RAY DIFFRACTION1A901 - 903
3X-RAY DIFFRACTION1A1001 - 1281

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