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- PDB-8f8k: The structure of Rv2173 from M. tuberculosis with IPP bound -

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Basic information

Entry
Database: PDB / ID: 8f8k
TitleThe structure of Rv2173 from M. tuberculosis with IPP bound
Components(2E,6E)-farnesyl diphosphate synthase
KeywordsTRANSFERASE / Rv2173 / M. tuberculosis / Isoprenyl diphosphate synthase / IPP (isopentenyl diphosphate) bound
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / dimethylallyltranstransferase activity / geranyltranstransferase activity / prenyltransferase 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
ACETATE ION / 3-METHYLBUT-3-ENYL TRIHYDROGEN 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. / Beasley, C.P.H.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,80412
Polymers41,9821
Non-polymers82211
Water1,65792
1
A: (2E,6E)-farnesyl diphosphate synthase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)85,60824
Polymers83,9632
Non-polymers1,64422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area9960 Å2
ΔGint-144 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.659, 82.692, 189.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein (2E,6E)-farnesyl diphosphate 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O53507

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Non-polymers , 6 types, 103 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M Tris, pH 7.5, 0.2 M calcium acetate, 20% PEG3350

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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: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→19.8 Å / Num. obs: 26593 / % possible obs: 99.9 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.051 / Rrim(I) all: 0.194 / Χ2: 1.05 / Net I/σ(I): 15.4 / Num. measured all: 389059
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 4.175 / Num. measured all: 33239 / Num. unique obs: 2255 / CC1/2: 0.359 / Rpim(I) all: 1.124 / Rrim(I) all: 4.325 / Χ2: 1.02 / 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→19.8 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1335 5.02 %
Rwork0.2083 --
obs0.2098 26577 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 46 92 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022750
X-RAY DIFFRACTIONf_angle_d0.4883735
X-RAY DIFFRACTIONf_dihedral_angle_d4.807405
X-RAY DIFFRACTIONf_chiral_restr0.032430
X-RAY DIFFRACTIONf_plane_restr0.006493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.40131480.37822449X-RAY DIFFRACTION100
2.28-2.370.30261190.31142498X-RAY DIFFRACTION100
2.37-2.480.3131330.30642475X-RAY DIFFRACTION100
2.48-2.610.29621330.2572503X-RAY DIFFRACTION100
2.61-2.770.2581410.24892503X-RAY DIFFRACTION100
2.77-2.980.23241070.23152553X-RAY DIFFRACTION100
2.98-3.280.25421310.21162519X-RAY DIFFRACTION100
3.28-3.760.2291360.19232531X-RAY DIFFRACTION100
3.76-4.720.19661460.17042549X-RAY DIFFRACTION100
4.72-19.80.22511410.17622662X-RAY DIFFRACTION100

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