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- PDB-3wql: Crystal structure of Rv3378c with Mg2+ and PPi -

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Basic information

Entry
Database: PDB / ID: 3wql
TitleCrystal structure of Rv3378c with Mg2+ and PPi
ComponentsDiterpene synthase
KeywordsHYDROLASE / phosphatase / diterpene synthase
Function / homology
Function and homology information


adenosine tuberculosinyltransferase / (13S)-vitexifolin A synthase activity / tuberculosinol biosynthetic process / diterpenoid biosynthetic process / response to host immune response / 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
Tuberculosinyl adenosine transferase / Tuberculosinyl adenosine transferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJan 28, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Diterpene synthase
B: Diterpene synthase
C: Diterpene synthase
D: Diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,48012
Polymers136,2864
Non-polymers1948
Water18,3391018
1
A: Diterpene synthase
B: Diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2406
Polymers68,1432
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7770 Å2
ΔGint-77 kcal/mol
Surface area25440 Å2
MethodPISA
2
C: Diterpene synthase
D: Diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2406
Polymers68,1432
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-77 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.420, 56.525, 114.435
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

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


Mass: 34071.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3378c, MT3488 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1018 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.26 %

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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: Nov 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 77301 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.3 / % possible all: 85.6

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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: 3WQK

3wqk


Resolution: 2.1→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.239 -
Rwork0.198 -
all-78294
obs-65562
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9245 0 8 1018 10271
LS refinement shellResolution: 2.1→2.2 Å /
RfactorNum. reflection
Rfree0.302 -
Rwork0.222 -
obs-2237

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