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- PDB-5iys: Crystal structure of a dehydrosqualene synthase in complex with ligand -

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Basic information

Entry
Database: PDB / ID: 5iys
TitleCrystal structure of a dehydrosqualene synthase in complex with ligand
ComponentsPhytoene synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / dehydrosqualene synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homologyfarnesyl-diphosphate farnesyltransferase activity / squalene synthase activity / Squalene/phytoene synthase / Trans-isoprenyl diphosphate synthases, head-to-head / Squalene/phytoene synthase / biosynthetic process / Isoprenoid synthase domain superfamily / Chem-FPS / Phytoene synthase
Function and homology information
Biological speciesEnterococcus hirae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsLiu, G.Z. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: to be published
Title: Crystal structure of a dehydrosqualene synthase in complex with ligand
Authors: Liu, G.Z. / Liu, W.D. / Chen, C.C. / Guo, R.T.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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_conn_angle / refine_hist / struct_conn
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.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.value / _refine_hist.d_res_high / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phytoene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8038
Polymers33,7421
Non-polymers1,0627
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.238, 41.090, 93.477
Angle α, β, γ (deg.)90.000, 96.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phytoene synthase / Uncharacterized protein


Mass: 33741.641 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258) (bacteria)
References: UniProt: I6T9U8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.11 Å3/Da / Density % sol: 41.61 % / Mosaicity: 0.726 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG 3350, 0.1M Li2SO4, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→25 Å / Num. obs: 21148 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.04 / Rrim(I) all: 0.076 / Χ2: 1.075 / Net I/av σ(I): 16.662 / Net I/σ(I): 13.7 / Num. measured all: 70500
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.93-23.30.258197.1
2-2.083.40.188199.2
2.08-2.173.40.137199.4
2.17-2.293.40.105199.2
2.29-2.433.40.086199
2.43-2.623.40.076198.8
2.62-2.883.30.065198.4
2.88-3.33.30.058197.9
3.3-4.153.20.052196.8
4.15-253.10.051194.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E9U

4e9u


Resolution: 1.93→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.356 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 1088 5.2 %RANDOM
Rwork0.1641 ---
obs0.1669 20009 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 76.05 Å2 / Biso mean: 29.324 Å2 / Biso min: 10.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.66 Å2
2---0.85 Å20 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.93→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 61 203 2589
Biso mean--39.6 40.14 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222427
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9933274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41724.262122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95115438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9691517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211839
X-RAY DIFFRACTIONr_mcbond_it1.761.51417
X-RAY DIFFRACTIONr_mcangle_it2.80122284
X-RAY DIFFRACTIONr_scbond_it4.89431010
X-RAY DIFFRACTIONr_scangle_it7.5114.5990
LS refinement shellResolution: 1.924→1.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 74 -
Rwork0.198 1391 -
all-1465 -
obs--91.45 %
Refinement TLS params.Method: refined / Origin x: 9.247 Å / Origin y: 9.2163 Å / Origin z: 25.0662 Å
111213212223313233
T0.0285 Å2-0.0081 Å20.0102 Å2-0.0393 Å2-0.0066 Å2--0.0408 Å2
L0.0678 °20.0485 °20.0792 °2-0.5615 °20.0074 °2--0.4682 °2
S-0.0312 Å °-0.0132 Å °-0.0033 Å °-0.0818 Å °0.0499 Å °-0.0222 Å °0.0092 Å °-0.0077 Å °-0.0187 Å °

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