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- PDB-6vsg: Mycobacterium tuberculosis dihydrofolate reductase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6vsg
TitleMycobacterium tuberculosis dihydrofolate reductase in complex with 4-(trifluoromethyl)benzene-1,2-diamine(fragment 17)
ComponentsDihydrofolate reductase
KeywordsBIOSYNTHETIC PROTEIN / folate pathway
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsRibeiro, J.A. / Dias, M.V.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/00351-1 Brazil
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase fromMycobacterium tuberculosis.
Authors: Ribeiro, J.A. / Hammer, A. / Libreros-Zuniga, G.A. / Chavez-Pacheco, S.M. / Tyrakis, P. / de Oliveira, G.S. / Kirkman, T. / El Bakali, J. / Rocco, S.A. / Sforca, M.L. / Parise-Filho, R. / ...Authors: Ribeiro, J.A. / Hammer, A. / Libreros-Zuniga, G.A. / Chavez-Pacheco, S.M. / Tyrakis, P. / de Oliveira, G.S. / Kirkman, T. / El Bakali, J. / Rocco, S.A. / Sforca, M.L. / Parise-Filho, R. / Coyne, A.G. / Blundell, T.L. / Abell, C. / Dias, M.V.B.
History
DepositionFeb 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn.ptnr2_label_seq_id
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6598
Polymers35,7872
Non-polymers1,8736
Water3,603200
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0236
Polymers17,8931
Non-polymers1,1305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6372
Polymers17,8931
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-29 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.912, 70.701, 72.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase


Mass: 17893.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: folA, dfrA, Rv2763c, MTV002.28c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WNX1, dihydrofolate reductase

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Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-X0V / 4-(TRIFLUOROMETHYL)BENZENE-1,2-DIAMINE


Mass: 176.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7F3N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 1.6 M ammonium sulfate, 100 mM MES (2-(N-morpholino) ethanesulfonic acid), pH 6.5, 10 mM CoCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.48 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
Reflection twinOperator: -h,l,k / Fraction: 0.06
ReflectionResolution: 2.3→46.54 Å / Num. obs: 14223 / % possible obs: 99.1 % / Redundancy: 12.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.053 / Rrim(I) all: 0.187 / Net I/σ(I): 13.2 / Num. measured all: 174536
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3811.81.0361470412490.7780.3111.0832.691.4
8.92-46.5410.20.05230102960.9970.0170.05537.399.6

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1df7

1df7


Resolution: 2.304→46.539 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.42
RfactorNum. reflection% reflection
Rfree0.2223 685 4.83 %
Rwork0.1699 --
obs0.1717 14182 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.07 Å2 / Biso mean: 31.3692 Å2 / Biso min: 15.36 Å2
Refinement stepCycle: final / Resolution: 2.304→46.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 116 200 2800
Biso mean--33.5 38.6 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082667
X-RAY DIFFRACTIONf_angle_d0.913646
X-RAY DIFFRACTIONf_chiral_restr0.052386
X-RAY DIFFRACTIONf_plane_restr0.007462
X-RAY DIFFRACTIONf_dihedral_angle_d19.5241516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3074-2.48510.28261370.21632587272493
2.4851-2.73440.27621280.19722662279095
2.7344-3.12810.23891480.18182659280795
3.1281-3.93360.18421290.14852724285395
3.9336-17.47480.20061320.15492825295796
Refinement TLS params.Method: refined / Origin x: 53.4215 Å / Origin y: 70.5185 Å / Origin z: 18.3781 Å
111213212223313233
T0.2157 Å2-0.0014 Å20.0158 Å2-0.1956 Å2-0.0109 Å2--0.1713 Å2
L0.6551 °20.2101 °20.2024 °2-0.224 °2-0.0319 °2--0.1265 °2
S-0.0067 Å °0.0135 Å °-0.0402 Å °0.0241 Å °0.0058 Å °-0.0475 Å °-0.0063 Å °-0.0186 Å °0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 159
2X-RAY DIFFRACTION1allB1 - 159
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allS1 - 190
8X-RAY DIFFRACTION1allS191 - 200

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