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- PDB-5qtd: Unliganded T. brucei FPPS -

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Basic information

Entry
Database: PDB / ID: 5qtd
TitleUnliganded T. brucei FPPS
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / farnesyl diphosphate synthase / Trypanosoma brucei / PanDDA / protein-ligand complex
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.642 Å
AuthorsMuenzker, L. / Petrick, J.K. / Schleberger, C. / Cornaciu, I. / Marquez, J.A. / Jahnke, W.
CitationJournal: To Be Published
Title: Unliganded T. brucei FPPS
Authors: Muenzker, L.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 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

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4745
Polymers42,1691
Non-polymers3054
Water2,126118
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,94810
Polymers84,3382
Non-polymers6108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7420 Å2
ΔGint-94 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.453, 60.453, 340.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-544-

HOH

21A-582-

HOH

31A-613-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 42169.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86C09
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.13 Å3/Da / Density % sol: 42.17 % / Mosaicity: 0.09 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.12 M CsCl 12 % w/v PEG 3350, 12 % v/v DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.642→56.678 Å / Num. obs: 27755 / % possible obs: 59.6 % / Redundancy: 36.1 % / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.017 / Rrim(I) all: 0.1 / Rsym value: 0.13 / Net I/σ(I): 24 / Num. measured all: 715057 / Scaling rejects: 1
Reflection shellResolution: 1.642→1.86 Å / Redundancy: 34.8 % / Rmerge(I) obs: 2.59 / Mean I/σ(I) obs: 1.6 / Num. measured all: 89508 / Num. unique obs: 2344 / CC1/2: 0.979 / Rpim(I) all: 0.143 / Rrim(I) all: 0.9 / Rsym value: 2.59 / Net I/σ(I) obs: 5.5 / % possible all: 9.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
XDS20180808data reduction
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4ryp

4ryp


Resolution: 1.642→56.678 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2979 1364 5 %
Rwork0.2502 25934 -
obs0.2526 27298 58.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.67 Å2 / Biso mean: 43.7054 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: final / Resolution: 1.642→56.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 17 118 2764
Biso mean--68.38 40.74 -
Num. residues----330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.642-1.7007110.399664651
1.7007-1.76880.4519140.35962752896
1.7688-1.84930.3175490.343182687519
1.8493-1.94680.4541660.48671295136130
1.9468-2.06880.41611060.3852197230351
2.0688-2.22850.33372040.3123729393385
2.2285-2.45280.33892070.29063901410889
2.4528-2.80770.33452320.273844594691100
2.8077-3.53740.29982390.240345214760100
3.5374-56.71140.24652470.19784667491496
Refinement TLS params.Method: refined / Origin x: 3.0635 Å / Origin y: 11.5786 Å / Origin z: -10.8889 Å
111213212223313233
T0.5598 Å20.0904 Å2-0.1398 Å2-0.3408 Å2-0.0461 Å2---0.0538 Å2
L0.3253 °20.2644 °20.1033 °2-1.0173 °20.8177 °2--1.4139 °2
S-0.3137 Å °0.2578 Å °-0.0037 Å °-0.8276 Å °0.018 Å °0.4568 Å °-1.0704 Å °-0.3449 Å °-0.5609 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 362
2X-RAY DIFFRACTION1allB3 - 501
3X-RAY DIFFRACTION1allS1 - 118

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