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- PDB-3wqm: Crystal structure of Rv3378c with inhibitor BPH-629 -

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Basic information

Entry
Database: PDB / ID: 3wqm
TitleCrystal structure of Rv3378c with inhibitor BPH-629
ComponentsDiterpene synthase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / diterpene synthase / HYDROLASE-HYDROLASE INHIBITOR complex
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-B29 / PHOSPHATE ION / 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 26, 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_ref_seq_dif / 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_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.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_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_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)35,5246
Polymers34,4131
Non-polymers1,1115
Water5,477304
1
A: Diterpene synthase
hetero molecules

A: Diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,04712
Polymers68,8262
Non-polymers2,22210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11710 Å2
ΔGint-95 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.417, 105.417, 65.991
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

21A-702-

HOH

31A-773-

HOH

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Components

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


Mass: 34412.844 Da / Num. of mol.: 1
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)
References: UniProt: O50407, UniProt: P9WJ61*PLUS, EC: 3.1.7.9, EC: 3.1.7.8
#2: Chemical ChemComp-B29 / [2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID / [2-(3-DIBENZO[B,D]FURAN-4-YLPHENYL)-1-HYDROXYETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)


Mass: 448.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18O8P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.66 Å3/Da / Density % sol: 53.82 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 21574 / % possible obs: 99.3 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 6.4 / % possible all: 97.6

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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
RfactorNum. reflection
Rfree0.237 -
Rwork0.197 -
all-21639
obs-20950
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 71 304 2757
LS refinement shellResolution: 2.1→2.2 Å / Num. reflection obs: 1961

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