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- PDB-6nne: Crystal structure of Dihydrofolate reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 6nne
TitleCrystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with diaverdine
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / antifolate
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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-KUP / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.595 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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

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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)37,83612
Polymers35,3222
Non-polymers2,51410
Water4,306239
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9186
Polymers17,6611
Non-polymers1,2575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9186
Polymers17,6611
Non-polymers1,2575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-73 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.663, 72.175, 72.381
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: 17660.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: dfrA, MRA_2788
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A5U6B6, dihydrofolate reductase

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Non-polymers , 5 types, 249 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-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-KUP / 5-[(3,4-dimethoxyphenyl)methyl]pyrimidine-2,4-diamine


Mass: 260.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 M Ammonium Sulphate, 10 mM cobalt chloride, 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: 1.59→46.94 Å / Num. obs: 43721 / % possible obs: 99.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 21.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Net I/σ(I): 12.9 / Num. measured all: 515905 / Scaling rejects: 105
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.59-1.62110.94321380.8010.2920.98896.2
8.59-46.9410.90.0863410.9950.0270.0999.4

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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: 1.595→32.351 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2188 2112 4.84 %
Rwork0.1775 41540 -
obs0.1794 43652 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.59 Å2 / Biso mean: 29.7927 Å2 / Biso min: 12.45 Å2
Refinement stepCycle: final / Resolution: 1.595→32.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 156 239 2879
Biso mean--26.74 39.63 -
Num. residues----318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5949-1.6320.31331410.26272667280897
1.632-1.67280.25711360.229527242860100
1.6728-1.7180.27971490.21327352884100
1.718-1.76860.24521390.200727432882100
1.7686-1.82560.20341130.190627612874100
1.8256-1.89090.22251340.191827432877100
1.8909-1.96660.2391590.185927292888100
1.9666-2.05610.2151760.184327272903100
2.0561-2.16440.20731560.178227382894100
2.1644-2.30.22881060.179327952901100
2.3-2.47750.22131550.182327662921100
2.4775-2.72680.25241230.186927902913100
2.7268-3.1210.19451330.180728092942100
3.121-3.93110.20671350.16428542989100
3.9311-32.35790.20891570.159229593116100
Refinement TLS params.Method: refined / Origin x: 23.0109 Å / Origin y: 0.1781 Å / Origin z: 17.7877 Å
111213212223313233
T0.1614 Å20.0002 Å2-0.0253 Å2-0.1374 Å2-0.0117 Å2--0.1288 Å2
L1.5157 °2-0.5637 °2-0.5552 °2-0.5214 °20.012 °2--0.3599 °2
S-0.0297 Å °-0.0115 Å °0.0241 Å °0.0042 Å °-0.0023 Å °-0.051 Å °0.0121 Å °0.0387 Å °0.0303 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 DIFFRACTION1allF1 - 2
6X-RAY DIFFRACTION1allS1 - 226
7X-RAY DIFFRACTION1allS227 - 241
8X-RAY DIFFRACTION1allS242
9X-RAY DIFFRACTION1allG1 - 4

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