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- PDB-5qpk: PanDDA analysis group deposition -- Crystal Structure of T. cruzi... -

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Basic information

Entry
Database: PDB / ID: 5qpk
TitlePanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000586a
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / membrane / metal ion binding
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / ~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.5 Å
AuthorsPetrick, J.K. / Nelson, E.R. / Muenzker, L. / Krojer, T. / Douangamath, A. / Brandao-Neto, J. / von Delft, F. / Dekker, C. / Jahnke, W.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition - FPPS screened against the DSI Fragment Library
Authors: Petrick, J.K. / Muenzker, L. / von Delft, F. / Jahnke, W.
History
DepositionMar 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9136
Polymers41,3601
Non-polymers5545
Water5,495305
1
A: Farnesyl diphosphate synthase
hetero molecules

A: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,82712
Polymers82,7192
Non-polymers1,10810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area7250 Å2
ΔGint-174 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.133, 58.133, 397.397
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Farnesyl diphosphate synthase


Mass: 41359.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WS26

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Non-polymers , 5 types, 310 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-LUY / ~{N}-(2-phenylethyl)-1~{H}-benzimidazol-2-amine


Mass: 237.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.51 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 80 mM MES, 4 mM ZnSO4, 12.36% w/v PEG MME 550, 11.57% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.5→198.72 Å / Num. obs: 65934 / % possible obs: 100 % / Redundancy: 16.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.018 / Rrim(I) all: 0.077 / Net I/σ(I): 16.8 / Num. measured all: 1102591 / Scaling rejects: 501
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.5411.92.115645447500.5240.6372.2061.3100
6.71-198.7214.10.057138319790.9980.0150.05945.899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1YHK

1yhk


Resolution: 1.5→66.23 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.086 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3361 5.2 %RANDOM
Rwork0.2028 ---
obs0.2046 61504 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.57 Å2 / Biso mean: 28.574 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å20 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.5→66.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 33 305 3209
Biso mean--40.57 41.21 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.024478
X-RAY DIFFRACTIONr_bond_other_d0.0020.023462
X-RAY DIFFRACTIONr_angle_refined_deg2.2411.9585298
X-RAY DIFFRACTIONr_angle_other_deg1.14938055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2725491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27724.18189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43815650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0311518
X-RAY DIFFRACTIONr_chiral_restr0.140.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024715
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02891
X-RAY DIFFRACTIONr_mcbond_it2.312.6342135
X-RAY DIFFRACTIONr_mcbond_other2.3242.6162097
X-RAY DIFFRACTIONr_mcangle_it3.1763.9312379
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 224 -
Rwork0.356 4443 -
all-4667 -
obs--98.27 %

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