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- PDB-3acx: Crystal structure of the C(30) carotenoid dehydrosqualene synthas... -

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Basic information

Entry
Database: PDB / ID: 3acx
TitleCrystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with BPH-673
ComponentsDehydrosqualene synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Transferase / Head-to-head condensation / Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


4,4'-diapophytoene synthase / carotenoid biosynthetic process / squalene synthase [NAD(P)H] activity / geranylgeranyl diphosphate synthase activity / metal ion binding
Similarity search - Function
Trans-isoprenyl diphosphate synthases, bacterial-type / Squalene/phytoene synthase, conserved site / Squalene and phytoene synthases signature 1. / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-673 / 4,4'-diapophytoene synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsLiu, C.I. / Jeng, W.Y. / Wang, A.H.J. / Oldfield, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism of action and inhibition of dehydrosqualene synthase
Authors: Lin, F.Y. / Liu, C.I. / Liu, Y.L. / Zhang, Y. / Wang, K. / Jeng, W.Y. / Ko, T.P. / Cao, R. / Wang, A.H.J. / Oldfield, E.
#1: Journal: Science / Year: 2008
Title: A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence.
Authors: Liu, C.I. / Liu, G.Y. / Song, Y. / Yin, F. / Hensler, M.E. / Jeng, W.Y. / Nizet, V. / Wang, A.H. / Oldfield, E.
#2: Journal: J.Med.Chem. / Year: 2009
Title: Inhibition of staphyloxanthin virulence factor biosynthesis in Staphylococcus aureus: in vitro, in vivo, and crystallographic results.
Authors: Song, Y. / Liu, C.I. / Lin, F.Y. / No, J.H. / Hensler, M. / Liu, Y.L. / Jeng, W.Y. / Low, J. / Liu, G.Y. / Nizet, V. / Wang, A.H. / Oldfield, E.
History
DepositionJan 13, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Dehydrosqualene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0972
Polymers34,7871
Non-polymers3091
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.628, 80.628, 90.453
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Dehydrosqualene synthase / Diapophytoene synthase / 4 / 4'-diapophytoene synthase / DAP synthase


Mass: 34787.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: ATCC 27659 / Gene: CrtM / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) pLysS
References: UniProt: A9JQL9, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-673 / N-(1-methylethyl)-3-[(3-prop-2-en-1-ylbiphenyl-4-yl)oxy]propan-1-amine


Mass: 309.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12-0.58M potassium sodium tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 25, 2008 / Details: Vertically Focusing Mirror
RadiationMonochromator: Horizontally Focusing Single Crystal Si(111) Bent Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97315 Å / Relative weight: 1
ReflectionResolution: 1.31→30 Å / Num. all: 82023 / Num. obs: 81916 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 66.3
Reflection shellResolution: 1.31→1.36 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 9.7 / Num. unique all: 8101 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCO

2zco


Resolution: 1.31→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.231 / SU ML: 0.024 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18181 4103 5 %RANDOM
Rwork0.15978 ---
obs0.16088 77731 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.31→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 23 453 2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222472
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9413331
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8955283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71124.275138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64115443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5411514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021898
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3031.51415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12522291
X-RAY DIFFRACTIONr_scbond_it2.90431057
X-RAY DIFFRACTIONr_scangle_it4.2914.51040
X-RAY DIFFRACTIONr_rigid_bond_restr1.56332472
X-RAY DIFFRACTIONr_sphericity_free5.3633453
X-RAY DIFFRACTIONr_sphericity_bonded4.24732415
LS refinement shellResolution: 1.31→1.381 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.194 598 -
Rwork0.155 11213 -
obs--99.99 %
Refinement TLS params.Method: refined / Origin x: 55.5295 Å / Origin y: 12.1679 Å / Origin z: 52.0644 Å
111213212223313233
T0.0001 Å20.0003 Å20.0007 Å2-0.004 Å20.0033 Å2--0.0106 Å2
L0.5112 °2-0.0399 °20.0967 °2-0.4325 °2-0.055 °2--0.6364 °2
S-0.0029 Å °-0.0255 Å °0.0081 Å °-0.0054 Å °0.0068 Å °-0.0361 Å °-0.004 Å °-0.027 Å °-0.0038 Å °

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