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- PDB-4cvy: Crystal structure of the M. tuberculosis sulfate ester dioxygenas... -

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Basic information

Entry
Database: PDB / ID: 4cvy
TitleCrystal structure of the M. tuberculosis sulfate ester dioxygenase Rv3406 in complex with iron.
ComponentsDIOXYGENASE RV3406/MT3514
KeywordsOXIDOREDUCTASE / DRUG DESIGN / DIOXYGENASE / DPRE1 / MYCOBACTERIAL ENZYMES
Function / homology
Function and homology information


alkyl sulfatase / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / 2-oxoglutarate-dependent dioxygenase activity / dioxygenase activity / response to antibiotic / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NITRATE ION / Alpha-ketoglutarate-dependent sulfate ester dioxygenase / Alpha-ketoglutarate-dependent sulfate ester dioxygenase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNeres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M. / Mori, G. / Farina, D. / Salina, S. / Makarov, V. / Kolly, G.S. ...Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M. / Mori, G. / Farina, D. / Salina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / Ferrari, S. / Brodin, P. / Delorme, V. / Landry, V. / de Jesus Lopes Ribeiro, A.L. / Saxena, P. / Pojer, F. / Venturelli, A. / Carta, A. / Luciani, R. / Porta, A. / Zanoni, G. / De Rossi, E. / Costi, M.P. / Riccardi, G. / Cole, S.T.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: 2-Carboxyquinoxalines Kill Mycobacterium Tuberculosis Through Noncovalent Inhibition of Dpre1.
Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / ...Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / Ferrari, S. / Brodin, P. / Delorme, V. / Landry, V. / De Jesus Lopes Ribeiro, A.L. / Farina, D. / Saxena, P. / Pojer, F. / Carta, A. / Luciani, R. / Porta, A. / Zanoni, G. / De Rossi, E. / Costi, M.P. / Riccardi, G. / Cole, S.T.
History
DepositionMar 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIOXYGENASE RV3406/MT3514
B: DIOXYGENASE RV3406/MT3514
C: DIOXYGENASE RV3406/MT3514
D: DIOXYGENASE RV3406/MT3514
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7619
Polymers130,4754
Non-polymers2855
Water3,387188
1
A: DIOXYGENASE RV3406/MT3514
C: DIOXYGENASE RV3406/MT3514
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4115
Polymers65,2382
Non-polymers1743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-34.8 kcal/mol
Surface area20520 Å2
MethodPISA
2
B: DIOXYGENASE RV3406/MT3514
D: DIOXYGENASE RV3406/MT3514
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3494
Polymers65,2382
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-34.9 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.970, 128.150, 138.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9419, 0.1835, -0.2814), (0.1915, -0.3948, -0.8986), (-0.276, -0.9002, 0.3367)-43.89, 4.891, -5.85
2given(-0.7449, -0.5815, -0.3271), (-0.575, 0.311, 0.7567), (-0.3383, 0.7518, -0.5661)-47.91, -40.08, 32.78
3given(0.6937, 0.4078, 0.5937), (0.3955, -0.9046, 0.1593), (0.602, 0.1243, -0.7887)-14.78, -17.99, 54.41

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Components

#1: Protein
DIOXYGENASE RV3406/MT3514


Mass: 32618.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P65075, UniProt: P9WKZ1*PLUS, Oxidoreductases
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 22% PEG2000, 300 MM MAGNESIUM NITRATE, 100 MM TRIS/HCL PH 8.0, 2% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98
DetectorType: PILATUS / Detector: PIXEL / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→43.4 Å / Num. obs: 74877 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.04 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FFA

4ffa


Resolution: 2→94.04 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.769 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25382 3773 5 %RANDOM
Rwork0.20765 ---
obs0.21 71028 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.837 Å2
Baniso -1Baniso -2Baniso -3
1-5.41 Å20 Å20 Å2
2---2.73 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2→94.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7466 0 8 188 7662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197647
X-RAY DIFFRACTIONr_bond_other_d0.0020.027247
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.93310420
X-RAY DIFFRACTIONr_angle_other_deg0.877316521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53722.781374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.675151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3551577
X-RAY DIFFRACTIONr_chiral_restr0.10.21168
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021881
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_it3.0583.7483792
X-RAY DIFFRACTIONr_mcbond_other3.0463.7463791
X-RAY DIFFRACTIONr_mcangle_it4.2925.5984719
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7694.1493855
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 266 -
Rwork0.324 5003 -
obs--94.6 %

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