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- PDB-4kt8: The complex structure of Rv3378c-Y51FY90F with substrate, TPP -

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Basic information

Entry
Database: PDB / ID: 4kt8
TitleThe complex structure of Rv3378c-Y51FY90F with substrate, TPP
ComponentsDiterpene synthase
KeywordsHYDROLASE / Diterpene synthase
Function / homology
Function and homology information


adenosine tuberculosinyltransferase / (13S)-vitexifolin A synthase activity / tuberculosinol biosynthetic process / diterpenoid biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / phosphatase activity
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9AX / PHOSPHATE ION / Tuberculosinyl adenosine transferase / Tuberculosinyl adenosine transferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChan, H.C. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Zheng, Y. / Bogue, S. / Nakano, C. / Hoshino, T. / Zhang, L. ...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.
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
DepositionMay 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 2.0Mar 14, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / struct_asym / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _struct_asym.entity_id / _struct_site.details
Revision 2.1Nov 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7755
Polymers34,0391
Non-polymers7354
Water99155
1
A: Diterpene synthase
hetero molecules

A: Diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,55010
Polymers68,0792
Non-polymers1,4718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area8730 Å2
ΔGint-94 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.287, 106.287, 66.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Diterpene synthase / Isotuberculosinol synthase / Nosyberkol synthase / Tuberculosinol synthase


Mass: 34039.484 Da / Num. of mol.: 1 / Mutation: Y51F, Y90F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3378c, MT3488 / Plasmid: pET32a Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 trx B
References: UniProt: O50407, UniProt: P9WJ61*PLUS, EC: 3.1.7.9, EC: 3.1.7.8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-9AX / (2E)-3-methyl-5-[(1R,2S,8aS)-1,2,5,5-tetramethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate


Mass: 450.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: obtained synthetically / 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: 2.77 Å3/Da / Density % sol: 55.58 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 15419 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 6.4 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VX5

3vx5
PDB Unreleased entry


Resolution: 2.4→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 -RANDOM
Rwork0.22 --
all-15450 -
obs-14914 -
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 44 55 2444
LS refinement shellResolution: 2.4→2.5 Å /
RfactorNum. reflection
Rfree0.3 -
Rwork0.276 -
obs-1326

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