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

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Basic information

Entry
Database: PDB / ID: 5qtc
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
DI(HYDROXYETHYL)ETHER / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.645 Å
AuthorsMuenzker, L. / Petrick, J.P. / Schleberger, C. / Jahnke, W.
CitationJournal: To Be Published
Title: Unliganded T. brucei FPPS
Authors: Muenzker, L.
History
DepositionAug 7, 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

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3533
Polymers42,1691
Non-polymers1842
Water2,612145
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7076
Polymers84,3382
Non-polymers3694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area6330 Å2
ΔGint-18 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.030, 60.030, 340.604
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-586-

HOH

21A-638-

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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.1 Å3/Da / Density % sol: 41.44 % / Mosaicity: 0.09 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20 % w/v PEG 3350, 0.2 M sodium tartrate dibasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.645→56.767 Å / Num. obs: 24792 / % possible obs: 54.1 % / Redundancy: 18 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.029 / Rrim(I) all: 0.127 / Rsym value: 0.092 / Net I/σ(I): 20.3 / Num. measured all: 628869
Reflection shellResolution: 1.645→1.878 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 1.9 / Num. measured all: 92960 / Num. unique obs: 5046 / CC1/2: 0.446 / Rpim(I) all: 2.228 / Rrim(I) all: 9.678 / Rsym value: 1.531 / Net I/σ(I) obs: 0.5 / % possible all: 8.4

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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: 1.645→56.767 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1234 4.98 %
Rwork0.2083 23548 -
obs0.2105 24782 54.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.81 Å2 / Biso mean: 44.3119 Å2 / Biso min: 15.62 Å2
Refinement stepCycle: final / Resolution: 1.645→56.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 11 145 2751
Biso mean--86.56 43.89 -
Num. residues----325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6446-1.71051.065220.35961061082
1.7105-1.78830.5202200.32893653858
1.7883-1.88260.2841430.306475079316
1.8826-2.00060.3367640.30591273133727
2.0006-2.1550.28311130.26232196230946
2.155-2.37190.31521990.25633794399379
2.3719-2.71510.29592550.231548515106100
2.7151-3.42070.25462590.210449215180100
3.4207-56.80120.21422790.178952925571100
Refinement TLS params.Method: refined / Origin x: 2.6547 Å / Origin y: 11.8524 Å / Origin z: -10.9774 Å
111213212223313233
T0.424 Å20.0687 Å2-0.0912 Å2-0.2353 Å2-0.0236 Å2--0.1394 Å2
L0.2527 °20.202 °2-0.3244 °2-1.0449 °21.4774 °2--2.8048 °2
S-0.0562 Å °0.0499 Å °-0.0314 Å °-0.4407 Å °-0.0651 Å °0.2403 Å °-0.7713 Å °-0.2357 Å °0.1768 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 363
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allS1 - 145

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