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- PDB-4s3d: IspG in complex with PPi -

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Basic information

Entry
Database: PDB / ID: 4s3d
TitleIspG in complex with PPi
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) / 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 protein / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / 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 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Dihydropteroate synthase-like / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 1.8 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 / 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_atom_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 1.3Dec 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)44,7483
Polymers44,2781
Non-polymers4702
Water4,197233
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)89,4966
Polymers88,5562
Non-polymers9394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7960 Å2
ΔGint-66 kcal/mol
Surface area30370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.020, 63.260, 86.530
Angle α, β, γ (deg.)90.00, 127.30, 90.00
Int Tables number5
Space group name H-MC121

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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 / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
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: 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: 1.8→30 Å / Num. all: 44509 / Num. obs: 43396 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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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: 1.8→15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.275 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19152 2170 5 %RANDOM
Rwork0.14145 ---
obs0.144 41225 97.91 %-
all-43395 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.964 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0 Å2-0.06 Å2
2--1.2 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 16 233 3325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193186
X-RAY DIFFRACTIONr_bond_other_d0.0010.023149
X-RAY DIFFRACTIONr_angle_refined_deg1.6522.0014326
X-RAY DIFFRACTIONr_angle_other_deg0.76637253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3545409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.622.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01215551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011533
X-RAY DIFFRACTIONr_chiral_restr0.0740.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02671
X-RAY DIFFRACTIONr_mcbond_it3.6052.9221624
X-RAY DIFFRACTIONr_mcbond_other3.6052.921623
X-RAY DIFFRACTIONr_mcangle_it4.2654.3862034
X-RAY DIFFRACTIONr_mcangle_other4.2654.3882035
X-RAY DIFFRACTIONr_scbond_it5.2523.4931562
X-RAY DIFFRACTIONr_scbond_other5.1743.4961545
X-RAY DIFFRACTIONr_scangle_other5.8595.0252263
X-RAY DIFFRACTIONr_long_range_B_refined5.73324.4373617
X-RAY DIFFRACTIONr_long_range_B_other5.63124.043528
X-RAY DIFFRACTIONr_rigid_bond_restr3.42836335
X-RAY DIFFRACTIONr_sphericity_free28.839576
X-RAY DIFFRACTIONr_sphericity_bonded14.59156429
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 157 -
Rwork0.32 2980 -
obs--97.97 %
Refinement TLS params.Method: refined / Origin x: -12.7213 Å / Origin y: 23.5687 Å / Origin z: 2.8429 Å
111213212223313233
T0.0104 Å2-0.0003 Å2-0.0033 Å2-0.0212 Å20.0004 Å2--0.0029 Å2
L0.0342 °2-0.0064 °20.0054 °2-0.002 °2-0.0005 °2--0.0455 °2
S0.0004 Å °-0.0025 Å °-0.0001 Å °-0 Å °0.001 Å °0.0011 Å °-0.0022 Å °-0.0048 Å °-0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 404
2X-RAY DIFFRACTION1A901 - 902
3X-RAY DIFFRACTION1A1001 - 1233

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