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- PDB-6nnh: Structure of Closed state of Dihydrofolate reductase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 6nnh
TitleStructure of Closed state of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with NADPH and cycloguanil
ComponentsDihydrofolate reductase
KeywordsBIOSYNTHETIC PROTEIN / antifolate
Function / homology
Function and homology information


dihydrofolate metabolic process / NADP+ binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1CY / : / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.523 Å
AuthorsGiudice, J.H.P. / Ribeiro, J.A. / Dias, M.V.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates.
Authors: Ribeiro, J.A. / Chavez-Pacheco, S.M. / de Oliveira, G.S. / Silva, C.D.S. / Giudice, J.H.P. / Libreros-Zuniga, G.A. / Dias, M.V.B.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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_ncs_dom_lim
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.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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)38,00714
Polymers35,3222
Non-polymers2,68512
Water6,053336
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0057
Polymers17,6611
Non-polymers1,3446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0017
Polymers17,6611
Non-polymers1,3406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-87 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.319, 71.245, 72.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 23 or resid 25...
21(chain B and (resid 1 through 23 or resid 25...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARG(chain A and (resid 1 through 23 or resid 25...AA1 - 231 - 23
12PROPROPHEPHE(chain A and (resid 1 through 23 or resid 25...AA25 - 3125 - 31
13GLUGLUGLUGLU(chain A and (resid 1 through 23 or resid 25...AA3333
14THRTHRTHRTHR(chain A and (resid 1 through 23 or resid 25...AA35 - 8735 - 87
15PROPROALAALA(chain A and (resid 1 through 23 or resid 25...AA89 - 10789 - 107
16ARGARGARGARG(chain A and (resid 1 through 23 or resid 25...AA109 - 158109 - 158
17SERSERSERSER(chain A and (resid 1 through 23 or resid 25...AA159159
18METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
19METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
110METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
111METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
112METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
21METMETARGARG(chain B and (resid 1 through 23 or resid 25...BB1 - 231 - 23
22PROPROPHEPHE(chain B and (resid 1 through 23 or resid 25...BB25 - 3125 - 31
23GLUGLUGLUGLU(chain B and (resid 1 through 23 or resid 25...BB3333
24THRTHRTHRTHR(chain B and (resid 1 through 23 or resid 25...BB35 - 8735 - 87
25PROPROALAALA(chain B and (resid 1 through 23 or resid 25...BB89 - 10789 - 107
26ARGARGSERSER(chain B and (resid 1 through 23 or resid 25...BB109 - 159109 - 159

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase /


Mass: 17660.992 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WNX1, dihydrofolate reductase

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Non-polymers , 6 types, 348 molecules

#2: Chemical ChemComp-1CY / 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine / Cycloguanil / Cycloguanil


Mass: 251.715 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14ClN5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor, antagonist*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.8 M Ammonium sulphate, 10 mM CoCl2, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 1.52→46.3 Å / Num. obs: 47946 / % possible obs: 99.1 % / Redundancy: 11.6 % / Biso Wilson estimate: 13.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.031 / Rrim(I) all: 0.107 / Net I/σ(I): 19.8 / Num. measured all: 557948 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.52-1.5560.89620530.7580.3890.98286.7
8.34-46.37.30.0873570.9870.0330.09399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
Aimless0.2.8data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NND

6nnd


Resolution: 1.523→10.638 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.4
RfactorNum. reflection% reflection
Rfree0.1986 2346 4.92 %
Rwork0.1696 --
obs0.171 47699 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.15 Å2 / Biso mean: 19.9358 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: final / Resolution: 1.523→10.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 163 336 2986
Biso mean--16.23 31.53 -
Num. residues----318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A920X-RAY DIFFRACTION6.129TORSIONAL
12B920X-RAY DIFFRACTION6.129TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5227-1.55370.28211270.25072306243387
1.5537-1.58740.25271340.21252562269697
1.5874-1.62420.24831510.190126562807100
1.6242-1.66470.1991390.186226742813100
1.6647-1.70950.22931220.177526652787100
1.7095-1.75960.22351370.170326562793100
1.7596-1.81610.21421390.168126712810100
1.8161-1.88070.19311400.168826792819100
1.8807-1.95550.19151450.161426622807100
1.9555-2.04390.20161360.166226692805100
2.0439-2.15090.17631580.168926782836100
2.1509-2.28440.19761460.167426742820100
2.2844-2.45870.18381390.165727152854100
2.4587-2.70250.22011600.168826692829100
2.7025-3.08520.17211370.171927432880100
3.0852-3.8560.18491200.154627722892100
3.856-10.63850.19551160.167429023018100
Refinement TLS params.Method: refined / Origin x: 22.5412 Å / Origin y: 0.0139 Å / Origin z: 17.6926 Å
111213212223313233
T0.0994 Å2-0.0026 Å2-0.0165 Å2-0.1155 Å2-0.0046 Å2--0.07 Å2
L0.8242 °2-0.2379 °2-0.3968 °2-0.2743 °20.0831 °2--0.1136 °2
S-0.0045 Å °-0.0133 Å °0.0103 Å °-0.0111 Å °0.001 Å °-0.0109 Å °-0.0035 Å °0.0161 Å °0.0051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD1 - 2
2X-RAY DIFFRACTION1allA1 - 159
3X-RAY DIFFRACTION1allB1 - 159
4X-RAY DIFFRACTION1allC1 - 2
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allE5
7X-RAY DIFFRACTION1allF1 - 2
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allS1 - 336

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