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- PDB-3aqc: M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in... -

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Basic information

Entry
Database: PDB / ID: 3aqc
TitleM. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium and FPP analogue
Components
  • Component A of hexaprenyl diphosphate synthase
  • Component B of hexaprenyl diphosphate synthase
KeywordsTRANSFERASE / Prenyltransferase
Function / homology
Function and homology information


hexaprenyl diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / hexaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) activity / menaquinone biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process / magnesium ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1450 / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1450 / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2DE / Hexaprenyl-diphosphate synthase small subunit ((2E,6E)-farnesyl-diphosphate specific) / Hexaprenyl-diphosphate synthase large subunit ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.61 Å
AuthorsSasaki, D. / Fujihashi, M. / Okuyama, N. / Kobayashi, Y. / Noike, M. / Koyama, T. / Miki, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation.
Authors: Sasaki, D. / Fujihashi, M. / Okuyama, N. / Kobayashi, Y. / Noike, M. / Koyama, T. / Miki, K.
History
DepositionOct 28, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: 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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Component A of hexaprenyl diphosphate synthase
B: Component B of hexaprenyl diphosphate synthase
C: Component A of hexaprenyl diphosphate synthase
D: Component B of hexaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,77213
Polymers108,8544
Non-polymers9189
Water1,24369
1
A: Component A of hexaprenyl diphosphate synthase
B: Component B of hexaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8686
Polymers54,4272
Non-polymers4414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-25 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: Component A of hexaprenyl diphosphate synthase
D: Component B of hexaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9047
Polymers54,4272
Non-polymers4775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-27 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.803, 189.803, 189.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Component A of hexaprenyl diphosphate synthase / Hexaprenyl diphosphate synthase small subunit


Mass: 17293.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus (bacteria) / Strain: B-P 26 / Gene: hexs-a / Plasmid: pET-32 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O66127, EC: 2.5.1.33
#2: Protein Component B of hexaprenyl diphosphate synthase / Hexaprenyl diphosphate synthase large subunit


Mass: 37133.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus (bacteria) / Strain: B-P 26 / Gene: hexs-b / Plasmid: pET-30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O66129, EC: 2.5.1.33

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Non-polymers , 4 types, 78 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-2DE / (2E,6E)-7,11-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 368.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26O7P2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.08M Tris-HCl (pH 8.5), 0.16M Magnesium chloride hexahydrate, 24% (w/v) PEG 4000, 20% (v/v) Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→133.63 Å / Num. obs: 34831 / % possible obs: 100 % / Redundancy: 15.9 % / Rsym value: 0.099 / Net I/σ(I): 27.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 9.1 / Rsym value: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0066phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.876 / SU B: 11.944 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28152 1744 5 %RANDOM
Rwork0.23823 ---
obs0.24039 32915 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.323 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7435 0 53 69 7557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0227619
X-RAY DIFFRACTIONr_angle_refined_deg0.6761.9610283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6285912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0924.415376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.536151395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6461542
X-RAY DIFFRACTIONr_chiral_restr0.050.21156
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025684
X-RAY DIFFRACTIONr_mcbond_it0.2961.54566
X-RAY DIFFRACTIONr_mcangle_it0.54927404
X-RAY DIFFRACTIONr_scbond_it0.56533053
X-RAY DIFFRACTIONr_scangle_it0.9854.52879
LS refinement shellResolution: 2.606→2.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 135 -
Rwork0.307 2431 -
obs--99.84 %

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