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- PDB-4e9z: Crystal structure of dehydrosqualene synthase (Crtm) from S. aure... -

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Basic information

Entry
Database: PDB / ID: 4e9z
TitleCrystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with quinuclidine BPH-651 in the S1 site
ComponentsDehydrosqualene synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / BPH-651 / 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-651 / 4,4'-diapophytoene synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsLin, F.-Y. / Liu, Y.-L. / Oldfield, E.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Head-to-Head Prenyl Tranferases: Anti-Infective Drug Targets.
Authors: Lin, F.Y. / Liu, Y.L. / Li, K. / Cao, R. / Zhu, W. / Axelson, J. / Pang, R. / Oldfield, E.
History
DepositionMar 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)34,6402
Polymers34,3611
Non-polymers2791
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.589, 80.589, 91.759
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 / 4 / 4'-diapophytoene synthase / DAP synthase / Diapophytoene synthase


Mass: 34361.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: crtM / Production host: Escherichia coli (E. coli) / References: UniProt: A9JQL9, 4,4'-diapophytoene synthase
#2: Chemical ChemComp-651 / (3R)-3-biphenyl-4-yl-1-azabicyclo[2.2.2]octan-3-ol


Mass: 279.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M POTASSIUM SODIUM TARTRATE, 20% W/ V PEG 3350, 1MM PPI, 1MM BPH-651 (LIGAND), pH 7.4, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. all: 21615 / Num. obs: 21594 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Rmerge(I) obs: 0.073

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Processing

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

2zco


Resolution: 2.06→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.466 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1093 5.1 %RANDOM
Rwork0.191 ---
obs0.193 20373 98.2 %-
all-20746 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 21 184 2597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222478
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9423346
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17324.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75315444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021905
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_it1.3151.51418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43522297
X-RAY DIFFRACTIONr_scbond_it3.94831060
X-RAY DIFFRACTIONr_scangle_it6.2274.51048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 59 -
Rwork0.208 1228 -
obs--80.29 %

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