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

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Basic information

Entry
Database: PDB / ID: 3adz
TitleCrystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with intermediate PSPP
ComponentsDehydrosqualene synthase
KeywordsTRANSFERASE / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Head-to-head condensation / Intermediate
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-PS7 / 4,4'-diapophytoene synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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. / 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.J. / Oldfield, E.
History
DepositionJan 31, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _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_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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dehydrosqualene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3314
Polymers34,6951
Non-polymers6353
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.685, 80.685, 90.794
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: 34695.402 Da / Num. of mol.: 1 / Mutation: Y129A
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-PS7 / {(1R,2R,3R)-2-[(3E)-4,8-dimethylnona-3,7-dien-1-yl]-2-methyl-3-[(1E,5E)-2,6,10-trimethylundeca-1,5,9-trien-1-yl]cyclopropyl}methyl trihydrogen diphosphate


Mass: 586.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H52O7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 11-21% PEG 4000, 0.3-0.4M MgCl2, 0.1M Tris, 0.5 mM PSPP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2009
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. all: 27854 / Num. obs: 27821 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 49.4
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2720 / % 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: 1.89→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.362 / SU ML: 0.087 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22236 1395 5 %RANDOM
Rwork0.1682 ---
obs0.17071 26389 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.272 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.52 Å20 Å2
2--1.05 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 41 263 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222479
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9483345
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1145283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56224.307137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68215442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9081514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021899
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_it1.3831.51415
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19822290
X-RAY DIFFRACTIONr_scbond_it3.32431064
X-RAY DIFFRACTIONr_scangle_it4.9644.51052
X-RAY DIFFRACTIONr_rigid_bond_restr2.22532479
X-RAY DIFFRACTIONr_sphericity_free6.9743265
X-RAY DIFFRACTIONr_sphericity_bonded3.65232424
LS refinement shellResolution: 1.89→1.992 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.245 191 -
Rwork0.181 3794 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 16.9124 Å / Origin y: 54.6636 Å / Origin z: 37.1044 Å
111213212223313233
T0.0141 Å20.0091 Å2-0.0123 Å2-0.0205 Å2-0.0022 Å2--0.0211 Å2
L1.2664 °20.2079 °2-0.3605 °2-1.0628 °2-0.2461 °2--2.0679 °2
S-0.0194 Å °0.0101 Å °0.0669 Å °0.0669 Å °-0.0474 Å °-0.0667 Å °0.0502 Å °0.1136 Å °0.0668 Å °

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