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- PDB-4e9u: Crystal structure of dehydrosqualene synthase (Crtm) from S. aure... -

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Basic information

Entry
Database: PDB / ID: 4e9u
TitleCrystal structure of dehydrosqualene synthase (Crtm) from S. aureus complexed with a thiocyanate inhibitor
ComponentsDehydrosqualene synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PRENYL TRANSFERASE / THIOCYANATE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


4,4'-diapophytoene synthase / carotenoid biosynthetic process / : / farnesyltranstransferase 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
2-(4-phenoxyphenoxy)ethyl thiocyanate / 4,4'-diapophytoene synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLin, F.-Y. / Axelson, J. / Liu, Y.-L. / Zhnag, Y. / 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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.ptnr3_label_seq_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_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)34,6573
Polymers34,3611
Non-polymers2962
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.440, 80.440, 90.793
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) / Strain (production host): BL21 / References: UniProt: A9JQL9, 4,4'-diapophytoene synthase
#2: Chemical ChemComp-RWY / 2-(4-phenoxyphenoxy)ethyl thiocyanate


Mass: 271.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NO2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: 0.75M POTASSIUM SODIUM TARTRATE, 1MM BPH-954 (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: Oct 28, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20218 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.77 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 20.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1010 5.17 %RANDOM
Rwork0.189 ---
all0.189 20227 --
obs0.191 19540 96.6 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.94 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4212 Å20 Å2-0 Å2
2--1.4212 Å20 Å2
3----2.8425 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 20 156 2568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072468
X-RAY DIFFRACTIONf_angle_d0.9623325
X-RAY DIFFRACTIONf_dihedral_angle_d13.31917
X-RAY DIFFRACTIONf_chiral_restr0.067347
X-RAY DIFFRACTIONf_plane_restr0.003427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21330.26531160.21792430X-RAY DIFFRACTION90
2.2133-2.35190.29241460.20452534X-RAY DIFFRACTION94
2.3519-2.53350.23751670.19772576X-RAY DIFFRACTION96
2.5335-2.78840.23961480.19532636X-RAY DIFFRACTION97
2.7884-3.19170.2381470.19782719X-RAY DIFFRACTION99
3.1917-4.02040.22671490.17262749X-RAY DIFFRACTION100
4.0204-36.7790.22221370.18482886X-RAY DIFFRACTION100

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