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- PDB-8f8l: The structure of Rv2173 from M. tuberculosis with DMAP bound -

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Basic information

Entry
Database: PDB / ID: 8f8l
TitleThe structure of Rv2173 from M. tuberculosis with DMAP bound
Components(2E,6E)-farnesyl diphosphate synthase
KeywordsTRANSFERASE / Rv2173 / M. tuberculosis / Isoprenyl diphosphate synthase / dimethylallyl diphosphate (DMAP) bound
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / isoprenoid biosynthetic process / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
DIMETHYLALLYL DIPHOSPHATE / (2E,6E)-farnesyl diphosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJohnston, J.M. / Allison, T.M. / Titterington, J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand) New Zealand
CitationJournal: To be Published
Title: The structure of Rv2173 from M. tuberculosis in APO-, IPP-, and DMAP-bound forms.
Authors: Johnston, J.M. / Allison, T.M. / Titterington, J. / Beasley, C.P.H.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (2E,6E)-farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4005
Polymers41,9821
Non-polymers4184
Water2,486138
1
A: (2E,6E)-farnesyl diphosphate synthase
hetero molecules

A: (2E,6E)-farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,80010
Polymers83,9632
Non-polymers8378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7190 Å2
ΔGint-89 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.841, 83.844, 188.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein (2E,6E)-farnesyl diphosphate synthase / E / E-FPP synthase / FPP synthase / Dimethylallyltranstransferase / Geranyl diphosphate synthase / ...E / E-FPP synthase / FPP synthase / Dimethylallyltranstransferase / Geranyl diphosphate synthase / GPP synthase


Mass: 41981.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: idsA2, Rv2173 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53507, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE / Dimethylallyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M Bicine-Tris, pH 8.3, 12.5% PEG4000, 25% glycerol, 0.03 M CA mix Ca/Mg

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→19.58 Å / Num. obs: 26527 / % possible obs: 97.2 % / Redundancy: 13.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.064 / Rrim(I) all: 0.238 / Χ2: 0.98 / Net I/σ(I): 12.6 / Num. measured all: 365883
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 82 % / Redundancy: 9.1 % / Rmerge(I) obs: 2.696 / Num. measured all: 18434 / Num. unique obs: 2016 / CC1/2: 0.238 / Rpim(I) all: 0.923 / Rrim(I) all: 2.861 / Χ2: 1.03 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
REFMAC5.0 (CCP4 8.0)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.58 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1336 5.04 %
Rwork0.2108 --
obs0.2124 26509 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 0 22 138 2763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022671
X-RAY DIFFRACTIONf_angle_d0.3773629
X-RAY DIFFRACTIONf_dihedral_angle_d12.78967
X-RAY DIFFRACTIONf_chiral_restr0.031418
X-RAY DIFFRACTIONf_plane_restr0.004475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.331280.32132059X-RAY DIFFRACTION81
2.28-2.370.32141210.29482332X-RAY DIFFRACTION91
2.37-2.480.31181380.28292544X-RAY DIFFRACTION99
2.48-2.610.27341200.25342558X-RAY DIFFRACTION100
2.61-2.770.28751410.23982577X-RAY DIFFRACTION100
2.77-2.980.2721210.23032571X-RAY DIFFRACTION100
2.98-3.280.28351350.22842594X-RAY DIFFRACTION100
3.28-3.750.24871400.20382591X-RAY DIFFRACTION100
3.76-4.720.18751480.16892613X-RAY DIFFRACTION100
4.72-19.580.20231440.17162734X-RAY DIFFRACTION100

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