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- PDB-4m2x: Mycobacterium tuberculosis dihydrofolate reductase complexed with... -

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Basic information

Entry
Database: PDB / ID: 4m2x
TitleMycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Structural Genomics / TB Structural Genomics Consortium / TBSGC / reductase / NADPH binding / Hydride transfer / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
ACETATE ION / Chem-NDP / PHOSPHATE ION / TRIMETREXATE / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsJung, H. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Selective inhibitors for dihydrofolate reductase from mycobacterium tuberculosis
Authors: Jung, H. / Sacchettini, J.C.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
C: Dihydrofolate reductase
E: Dihydrofolate reductase
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,63035
Polymers71,7734
Non-polymers5,85731
Water1,76598
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,50810
Polymers17,9431
Non-polymers1,5659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4139
Polymers17,9431
Non-polymers1,4708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4139
Polymers17,9431
Non-polymers1,4708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2957
Polymers17,9431
Non-polymers1,3526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.090, 64.838, 68.062
Angle α, β, γ (deg.)93.480, 94.100, 100.250
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ACEG

#1: Protein
Dihydrofolate reductase /


Mass: 17943.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: folA, dfrA, Rv2763c, MT2833, MTV002.28c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A546, UniProt: P9WNX1*PLUS, dihydrofolate reductase

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Non-polymers , 5 types, 129 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-TMQ / TRIMETREXATE / Trimetrexate


Mass: 370.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H24N5O3 / Comment: inhibitor*YM
#4: Chemical...
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 43.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 15% PEG 6000, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 18, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.26→67.7 Å / Num. obs: 27037 / % possible obs: 95.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.96 % / Biso Wilson estimate: 32.928 Å2 / Rmerge(I) obs: 0.069 / Χ2: 0.99 / Net I/σ(I): 7.2 / Scaling rejects: 400
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.26-2.341.950.2332.4515126241.0693.6
2.34-2.431.960.2122.8521226481.0294.3
2.43-2.551.960.1743.5526826741.0594.5
2.55-2.681.950.1543.8526626851.0295.1
2.68-2.851.950.1274.853762741195.4
2.85-3.071.950.0985.8526326810.9795.8
3.07-3.381.960.0688.2536027160.9196.3
3.38-3.861.960.05911.1541227400.9596.9
3.86-4.871.960.0514.2546727630.8997.4
4.87-67.71.960.04815.1550727650.9897.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.43 Å67.7 Å
Translation2.43 Å67.7 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
d*TREK9.7 W8RSSIdata reduction
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→30.8564 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7678 / σ(F): 0 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1374 5.09 %random
Rwork0.1965 ---
all-27011 --
obs-26999 95.61 %-
Solvent computationBsol: 45.869 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso max: 73.88 Å2 / Biso mean: 32.8138 Å2 / Biso min: 17.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.481 Å2-8.379 Å2-0.403 Å2
2---0.463 Å2-3.552 Å2
3---0.944 Å2
Refinement stepCycle: LAST / Resolution: 2.26→30.8564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 393 98 5467
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.681
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.0461
X-RAY DIFFRACTIONf_dihedral_angle_d16.1031
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0831
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.26-2.2750.2716481X-RAY DIFFRACTION5189
2.275-2.29040.2569469X-RAY DIFFRACTION5189
2.2904-2.30610.2594501X-RAY DIFFRACTION5191
2.3061-2.32240.2556475X-RAY DIFFRACTION5189
2.3224-2.33910.2496517X-RAY DIFFRACTION5187
2.3391-2.35630.2374491X-RAY DIFFRACTION5191
2.3563-2.3740.2445494X-RAY DIFFRACTION5187
2.374-2.39220.2339502X-RAY DIFFRACTION5190
2.3922-2.41110.2479522X-RAY DIFFRACTION5189
2.4111-2.43050.2228469X-RAY DIFFRACTION5190
2.4305-2.45060.2273485X-RAY DIFFRACTION5191
2.4506-2.47130.2253502X-RAY DIFFRACTION5189
2.4713-2.49280.2176485X-RAY DIFFRACTION5189
2.4928-2.51510.2238507X-RAY DIFFRACTION5190
2.5151-2.53810.2212482X-RAY DIFFRACTION5190
2.5381-2.56210.2132536X-RAY DIFFRACTION5189
2.5621-2.58690.2149498X-RAY DIFFRACTION5192
2.5869-2.61280.2145473X-RAY DIFFRACTION5191
2.6128-2.63970.2022511X-RAY DIFFRACTION5190
2.6397-2.66780.2123479X-RAY DIFFRACTION5191
2.6678-2.69710.2074531X-RAY DIFFRACTION5191
2.6971-2.72770.2114513X-RAY DIFFRACTION5193
2.7277-2.75980.2211522X-RAY DIFFRACTION5191
2.7598-2.79340.2067490X-RAY DIFFRACTION5191
2.7934-2.82870.216519X-RAY DIFFRACTION5191
2.8287-2.86590.2119472X-RAY DIFFRACTION5191
2.8659-2.90520.229476X-RAY DIFFRACTION5190
2.9052-2.94660.2151557X-RAY DIFFRACTION5192
2.9466-2.99060.186495X-RAY DIFFRACTION5191
2.9906-3.03730.2002496X-RAY DIFFRACTION5191
3.0373-3.0870.1956502X-RAY DIFFRACTION5192
3.087-3.14020.189491X-RAY DIFFRACTION5191
3.1402-3.19720.1999522X-RAY DIFFRACTION5191
3.1972-3.25870.1932525X-RAY DIFFRACTION5190
3.2587-3.32510.1681465X-RAY DIFFRACTION5192
3.3251-3.39730.1906519X-RAY DIFFRACTION5190
3.3973-3.47630.1854484X-RAY DIFFRACTION5191
3.4763-3.56310.1816539X-RAY DIFFRACTION5192
3.5631-3.65930.164505X-RAY DIFFRACTION5191
3.6593-3.76670.1649506X-RAY DIFFRACTION5192
3.7667-3.88810.1609496X-RAY DIFFRACTION5192
3.8881-4.02680.1607532X-RAY DIFFRACTION5193
4.0268-4.18760.1506494X-RAY DIFFRACTION5191
4.1876-4.37770.1434510X-RAY DIFFRACTION5192
4.3777-4.60780.1408524X-RAY DIFFRACTION5193
4.6078-4.89540.1488505X-RAY DIFFRACTION5194
4.8954-5.27170.1814535X-RAY DIFFRACTION5193
5.2717-5.7990.1888499X-RAY DIFFRACTION5192
5.799-6.63090.2141504X-RAY DIFFRACTION5192
6.6309-8.3270.1714518X-RAY DIFFRACTION5193
8.327-30.85930.1611500X-RAY DIFFRACTION5190

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