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- PDB-2zy1: Crystal structure of the C(30) carotenoid dehydrosqualene synthas... -

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Basic information

Entry
Database: PDB / ID: 2zy1
TitleCrystal structure of the C(30) carotenoid dehydrosqualene synthase from Staphylococcus aureus complexed with bisphosphonate BPH-830
ComponentsDehydrosqualene synthase
KeywordsTRANSFERASE / CrtM / Carotenoid biosynthesis / Staphyloxanthin biosynthesis / Head-to-head condensation / Inhibitor
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-830 / 4,4'-diapophytoene synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLiu, C.I. / Jeng, W.Y. / Wang, A.H.J. / Oldfield, E.
Citation
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.
#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.
History
DepositionJan 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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

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Assembly

Deposited unit
A: Dehydrosqualene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2132
Polymers34,7871
Non-polymers4251
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.590, 80.590, 90.020
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-512-

HOH

21A-614-

HOH

31A-643-

HOH

41A-665-

HOH

51A-712-

HOH

61A-788-

HOH

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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-830 / dipotassium (2-oxo-2-{[3-(3-phenoxyphenyl)propyl]amino}ethyl)phosphonate


Mass: 425.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18K2NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2008
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: 1.78→30 Å / Num. all: 32866 / Num. obs: 32804 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 51.7
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3224 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCO

2zco


Resolution: 1.78→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1566 -random
Rwork0.182 ---
all-32866 --
obs-31532 95.9 %-
Displacement parametersBiso mean: 33.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 24 505 2882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 1.78→1.84 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.237 141 -
Rwork0.229 --
obs-2840 88.09 %

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