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- PDB-3vjd: Crystal structure of the Y248A mutant of C(30) carotenoid dehydro... -

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Basic information

Entry
Database: PDB / ID: 3vjd
TitleCrystal structure of the Y248A mutant of C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus
ComponentsDehydrosqualene synthase
KeywordsTRANSFERASE / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Head-to-head condensation
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
L(+)-TARTARIC ACID / 4,4'-diapophytoene synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLiu, C.I. / Jeng, W.Y. / Chang, W.J. / Wang, A.H.J.
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase
Authors: Liu, C.I. / Jeng, W.Y. / Chang, W.J. / Ko, T.P. / Wang, A.H.J.
#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.J. / 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.
#3: 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.
History
DepositionOct 14, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 8, 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_special_symmetry / 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)34,8452
Polymers34,6951
Non-polymers1501
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.587, 79.587, 90.757
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-724-

HOH

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Components

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


Mass: 34695.402 Da / Num. of mol.: 1 / Mutation: Y248A
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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.12-0.58M potassium sodium tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2010 / Details: HORIZONTAL FOCUSING MIRROR
RadiationMonochromator: LN2-Cooled Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 55854 / Num. obs: 55684 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.2 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 50.3
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4.2 / Num. unique all: 5523 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZCO

2zco


Resolution: 1.48→27.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.145 / SU ML: 0.038 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20559 2820 5.1 %RANDOM
Rwork0.16214 ---
obs0.16427 55539 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.48→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 10 335 2730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222500
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9353385
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11424.366142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66615455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8281515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021935
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_it1.5141.51439
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45922341
X-RAY DIFFRACTIONr_scbond_it3.89231061
X-RAY DIFFRACTIONr_scangle_it5.794.51036
X-RAY DIFFRACTIONr_rigid_bond_restr1.75732500
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.56 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.202 418 -
Rwork0.149 7632 -
obs-8050 99.74 %
Refinement TLS params.Method: refined / Origin x: 16.5671 Å / Origin y: 53.7061 Å / Origin z: 36.9076 Å
111213212223313233
T0.0024 Å2-0.0015 Å2-0.0015 Å2-0.0087 Å20.0082 Å2--0.0182 Å2
L0.644 °20.2715 °2-0.2042 °2-0.5981 °2-0.3884 °2--1.0571 °2
S-0.0223 Å °-0.0113 Å °0.0187 Å °-0.0005 Å °-0.0451 Å °-0.0466 Å °-0.0225 Å °0.0893 Å °0.0673 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 284
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 735

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