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- PDB-4onc: Crystal Structure of Mycobacterium Tuberculosis Decaprenyl Diphos... -

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Basic information

Entry
Database: PDB / ID: 4onc
TitleCrystal Structure of Mycobacterium Tuberculosis Decaprenyl Diphosphate Synthase in Complex with BPH-640
ComponentsDecaprenyl diphosphate synthase
KeywordsTRANSFERASE / polyprenyl transferase / decaprenyl diphosphate synthase
Function / homology
Function and homology information


trans,polycis-decaprenyl diphosphate synthase / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / Z-farnesyl diphosphate synthase activity / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / prenyltransferase activity / manganese ion binding / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-40B / Decaprenyl diphosphate synthase / Decaprenyl diphosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsFeng, X. / Chan, H.C. / Ko, T.P.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Structure and Inhibition of Tuberculosinol Synthase and Decaprenyl Diphosphate Synthase from Mycobacterium tuberculosis
Authors: Chan, H.C. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Zheng, Y. / Bogue, S. / Nakano, C. / Hoshino, T. / Zhang, L. / Lv, P. / Liu, W. / Crick, D.C. / Liang, P.H. / Wang, A.H. / Oldfield, E. / Guo, R.T.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decaprenyl diphosphate synthase
B: Decaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7624
Polymers64,9222
Non-polymers8412
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-12 kcal/mol
Surface area23400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.809, 89.167, 93.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Decaprenyl diphosphate synthase / DecaPP / Decaprenyl pyrophosphate synthase / Long-chain isoprenyl diphosphate synthase / Trans / ...DecaPP / Decaprenyl pyrophosphate synthase / Long-chain isoprenyl diphosphate synthase / Trans / polycis-decaprenyl diphosphate synthase


Mass: 32460.809 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 13-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2361c / Production host: Escherichia coli (E. coli)
References: UniProt: P60479, UniProt: P9WFF7*PLUS, trans,polycis-decaprenyl diphosphate synthase, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
#2: Chemical ChemComp-40B / [hydroxy(1,1':3',1''-terphenyl-3-yl)methanediyl]bis(phosphonic acid)


Mass: 420.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10% GLYCEROL, 25% PEG 400, 7% PEG 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 58370 / % possible obs: 100 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.83→1.86 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CCP4model building
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VG4

2vg4


Resolution: 1.83→49.73 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.36 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2945 5.1 %RANDOM
Rwork0.157 ---
obs0.159 55357 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-0 Å2
2---0.96 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.83→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 0 44 437 4991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194674
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.9616366
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93421.818231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0315750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7791564
X-RAY DIFFRACTIONr_chiral_restr0.1860.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 200 -
Rwork0.227 3783 -
obs--99.08 %

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