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- PDB-3tfp: Crystal Structure of Dehydrosqualene Synthase (CrtM) from S. aure... -

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Basic information

Entry
Database: PDB / ID: 3tfp
TitleCrystal Structure of Dehydrosqualene Synthase (CrtM) from S. aureus Complexed with BPH-1162
ComponentsDehydrosqualene synthase
KeywordsTRANSFERASE/transferase inhibitor / Head-to-Head Prenyl Synthase / 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-03L / 4,4'-diapophytoene synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, F.-Y. / Liu, Y.-L. / Zhang, Y. / Oldfield, E.
CitationJournal: Chemmedchem / Year: 2012
Title: Dual dehydrosqualene/squalene synthase inhibitors: leads for innate immune system-based therapeutics.
Authors: Lin, F.Y. / Zhang, Y. / Hensler, M. / Liu, Y.L. / Chow, O.A. / Zhu, W. / Wang, K. / Pang, R. / Thienphrapa, W. / Nizet, V. / Oldfield, E.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 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 / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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

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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)35,3034
Polymers34,7871
Non-polymers5153
Water3,261181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.246, 80.246, 92.196
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: 34787.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: crtM / Plasmid: pET32-LIC / Production host: Escherichia coli (E. coli)
References: UniProt: A9JQL9, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-03L / 2-({2-chloro-6-[(2,4-dichlorophenyl)sulfanyl]benzyl}carbamoyl)benzoic acid


Mass: 466.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14Cl3NO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 50.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M Potassium sodium tartrate, 20% w/v PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 26359 / Num. obs: 26333 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.9
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.3 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZCQ

2zcq


Resolution: 2→28.106 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1187 5.07 %RANDOM
Rwork0.1917 ---
obs0.1942 23418 98.9 %-
all-22678 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.986 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1513 Å20 Å2-0 Å2
2--1.1513 Å20 Å2
3----2.3026 Å2
Refinement stepCycle: LAST / Resolution: 2→28.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 31 181 2604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052485
X-RAY DIFFRACTIONf_angle_d0.8463354
X-RAY DIFFRACTIONf_dihedral_angle_d13.958930
X-RAY DIFFRACTIONf_chiral_restr0.059348
X-RAY DIFFRACTIONf_plane_restr0.003432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.27151440.20382646X-RAY DIFFRACTION96
2.091-2.20120.27561520.18962710X-RAY DIFFRACTION98
2.2012-2.33910.23581360.19862749X-RAY DIFFRACTION98
2.3391-2.51960.2261510.19182755X-RAY DIFFRACTION99
2.5196-2.77290.22961390.19962788X-RAY DIFFRACTION100
2.7729-3.17370.2641440.20772806X-RAY DIFFRACTION100
3.1737-3.99670.23721640.18522832X-RAY DIFFRACTION100
3.9967-28.10920.22981570.18192945X-RAY DIFFRACTION100

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