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- PDB-6nnc: Structure of Dihydrofolate reductase from Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 6nnc
TitleStructure of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with NADPH and pemetrexed
ComponentsDihydrofolate reductase
KeywordsBIOSYNTHETIC PROTEIN / antifolate
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
: / Chem-LYA / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsRibeiro, J.A. / Chavez-Pacheco, S.M. / 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 14, 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 1.2Mar 13, 2024Group: 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_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_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)38,17012
Polymers35,3222
Non-polymers2,84810
Water5,693316
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0856
Polymers17,6611
Non-polymers1,4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0856
Polymers17,6611
Non-polymers1,4245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-74 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.346, 70.718, 72.216
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 154 or resid 156 through 159))
21(chain B and (resid 1 through 154 or resid 156 through 159))

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
11METMETTYRTYR(chain A and (resid 1 through 154 or resid 156 through 159))AA1 - 1541 - 154
12TYRTYRSERSER(chain A and (resid 1 through 154 or resid 156 through 159))AA156 - 159156 - 159
21METMETTYRTYR(chain B and (resid 1 through 154 or resid 156 through 159))BB1 - 1541 - 154
22TYRTYRSERSER(chain B and (resid 1 through 154 or resid 156 through 159))BB156 - 159156 - 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 (E. coli) / References: UniProt: P9WNX1, dihydrofolate reductase

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Non-polymers , 5 types, 326 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-LYA / 2-{4-[2-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-5-YL)-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID / LY231514


Mass: 427.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N5O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 M ammonium sulphate, 100 mM MES, 10 mM cobalt chloride

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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: 1.8→46.75 Å / Num. obs: 29295 / % possible obs: 98.4 % / Redundancy: 12.6 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Net I/σ(I): 29.7 / Num. measured all: 368144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.84110.41715750.950.1290.43791.6
1.8-46.7510.60.0462900.9950.0150.04899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260)refinement
XDSdata reduction
Aimless0.2.8data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.159 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 1485 5.08 %
Rwork0.1605 27749 -
obs0.1627 29234 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.89 Å2 / Biso mean: 26.1637 Å2 / Biso min: 10.13 Å2
Refinement stepCycle: final / Resolution: 1.8→32.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 180 316 2984
Biso mean--23.98 37.3 -
Num. residues----318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A972X-RAY DIFFRACTION8.008TORSIONAL
12B972X-RAY DIFFRACTION8.008TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.85810.23661140.18382337245192
1.8581-1.92450.21271300.17112380251096
1.9245-2.00160.23011540.16942476263098
2.0016-2.09260.23971260.17652499262598
2.0926-2.20290.2081420.16842521266399
2.2029-2.34090.20461200.16342524264499
2.3409-2.52160.19521400.16112535267599
2.5216-2.77520.2041390.166825542693100
2.7752-3.17650.21361330.162325882721100
3.1765-4.00090.18961490.149625992748100
4.0009-32.16370.19351380.15132736287499
Refinement TLS params.Method: refined / Origin x: 22.9291 Å / Origin y: 0.1282 Å / Origin z: 17.7536 Å
111213212223313233
T0.1444 Å2-0.0093 Å2-0.0296 Å2-0.1238 Å2-0.0103 Å2--0.1161 Å2
L1.1986 °2-0.4486 °2-0.4724 °2-0.4743 °20.0551 °2--0.2465 °2
S0.0024 Å °-0.0102 Å °0.0593 Å °-0.0118 Å °-0.0063 Å °-0.0711 Å °-0.0065 Å °0.0114 Å °0.0011 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 - 2
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allS1 - 306
7X-RAY DIFFRACTION1allS307 - 318
8X-RAY DIFFRACTION1allF1 - 4

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