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- PDB-3noy: Crystal structure of IspG (gcpE) -

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Basic information

Entry
Database: PDB / ID: 3noy
TitleCrystal structure of IspG (gcpE)
Components4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
KeywordsOXIDOREDUCTASE / Iron-sulfur protein / non-mevalonate pathway / terpene biosynthesis / isoprenoid biosynthesis / TIM-barrel N-domain / Ferredoxin C-domain / Converts 2C-methyl-D-erythritol 2 / 4-cyclodiphosphate (ME-2 / 4cPP) / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate / Cytosol
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 / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Dihydropteroate synthase-like / Dihydropteroate synthase-like / Enolase-like, C-terminal domain superfamily / 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 / Dihydropteroate synthase-like / Dihydropteroate synthase-like / Enolase-like, C-terminal domain superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsGroll, M. / Graewert, T. / Bacher, A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Biosynthesis of isoprenoids: crystal structure of the [4Fe-4S] cluster protein IspG.
Authors: Lee, M. / Grawert, T. / Quitterer, F. / Rohdich, F. / Eppinger, J. / Eisenreich, W. / Bacher, A. / Groll, M.
History
DepositionJun 26, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,5658
Polymers161,1594
Non-polymers1,4074
Water4,450247
1
A: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
B: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2834
Polymers80,5792
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-36 kcal/mol
Surface area30070 Å2
MethodPISA
2
C: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
D: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2834
Polymers80,5792
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-32 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.700, 119.010, 63.820
Angle α, β, γ (deg.)90.00, 95.48, 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: 40289.637 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1540, gcpE, ispG / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O67496, EC: 1.17.7.1
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100mM Bis-Tris, 9% PEG 8000, 17mM SrCl2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.7362, 1.7421, 1.7122
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: Plane Grating Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73621
21.74211
31.71221
ReflectionResolution: 2.6→30 Å / Num. obs: 55518 / % possible obs: 99.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.068 / Net I/σ(I): 19
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.5 / Num. unique all: 10138 / Rsym value: 0.525 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 30.803 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26614 2478 5 %RANDOM
Rwork0.22147 ---
all0.22375 47122 --
obs0.22375 47078 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.809 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å20 Å2-1.28 Å2
2--2.29 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10787 0 32 247 11066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211003
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.98714836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9951397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5524.207435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.387152100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.431580
X-RAY DIFFRACTIONr_chiral_restr0.0690.21729
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217932
X-RAY DIFFRACTIONr_mcbond_it0.4681.56925
X-RAY DIFFRACTIONr_mcangle_it0.844211208
X-RAY DIFFRACTIONr_scbond_it0.63834078
X-RAY DIFFRACTIONr_scangle_it1.1454.53580
X-RAY DIFFRACTIONr_rigid_bond_restr0.518311003
X-RAY DIFFRACTIONr_sphericity_free0.8583247
X-RAY DIFFRACTIONr_sphericity_bonded0.273310819
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 180 -
Rwork0.275 3420 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6782-0.13940.71260.3314-0.42981.29040.00270.03230.037-0.0636-0.0720.06330.0950.24480.06920.21840.06530.03780.16490.03160.1109-39.04417.71727.563
21.5409-0.55330.73030.349-0.37131.2929-0.0444-0.07840.30190.0593-0.0178-0.0936-0.18730.30650.06220.1874-0.0498-0.02180.2214-0.01250.1757-30.78341.63545.646
31.50990.4312-0.4980.2096-0.31450.54540.0958-0.0266-0.0811-0.0006-0.05210.0353-0.01230.1444-0.04380.242-0.0449-0.01280.1378-0.05220.1655-41.257-10.0399.358
42.08511.0261-0.13230.593-0.12830.62080.05730.1082-0.5355-0.060.0996-0.29040.22130.2176-0.15690.32840.0789-0.00320.165-0.17580.3434-30.461-34.502-6.706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 349
2X-RAY DIFFRACTION2B1 - 351
3X-RAY DIFFRACTION3C1 - 351
4X-RAY DIFFRACTION4D2 - 351

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