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- PDB-6cxm: Crystal structure of a dihydrofolate reductase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 6cxm
TitleCrystal structure of a dihydrofolate reductase from Mycobacterium smegmatis in complex with NADP and P218
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/INHIBITOR / NIAID / National Institute of Allergy and Infectious Disease / structural genomics / Mycobacterium tuberculosis / Mtb / inhibitor / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OXIDOREDUCTASE-INHIBITOR complex
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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a dihydrofolate reductase from Mycobacterium smegmatis in complex with NADP and P218
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionApr 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)39,1536
Polymers36,9462
Non-polymers2,2084
Water86548
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5773
Polymers18,4731
Non-polymers1,1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5773
Polymers18,4731
Non-polymers1,1042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.250, 40.300, 67.220
Angle α, β, γ (deg.)90.000, 93.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 74 or (resid 75...
21(chain B and (resid 2 through 33 or (resid 34...

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
11SERSERALAALA(chain A and (resid 2 through 74 or (resid 75...AA2 - 7410 - 82
12GLUGLUGLUGLU(chain A and (resid 2 through 74 or (resid 75...AA7583
13SERSERARGARG(chain A and (resid 2 through 74 or (resid 75...AA2 - 15610 - 164
14SERSERARGARG(chain A and (resid 2 through 74 or (resid 75...AA2 - 15610 - 164
15SERSERARGARG(chain A and (resid 2 through 74 or (resid 75...AA2 - 15610 - 164
21SERSERLYSLYS(chain B and (resid 2 through 33 or (resid 34...BB2 - 3310 - 41
22GLUGLUGLUGLU(chain B and (resid 2 through 33 or (resid 34...BB3442
23SERSERARGARG(chain B and (resid 2 through 33 or (resid 34...BB2 - 15610 - 164
24SERSERARGARG(chain B and (resid 2 through 33 or (resid 34...BB2 - 15610 - 164
25SERSERARGARG(chain B and (resid 2 through 33 or (resid 34...BB2 - 15610 - 164

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Components

#1: Protein Dihydrofolate reductase


Mass: 18472.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: folA, MSMEI_2607 / Production host: Escherichia coli (E. coli) / References: UniProt: I7FC10, dihydrofolate reductase
#2: 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
#3: Chemical ChemComp-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid


Mass: 360.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: MysmA.01062.a.B1.PS38260 at 8.81 mg/mL with 3 mM NADP and 3 mM P218 against MCSG1 screen condition G6 0.1 M sodium acetate pH 4.5, 25% PEG 3350 supplemented with 15% ethylene glycol as cryo- ...Details: MysmA.01062.a.B1.PS38260 at 8.81 mg/mL with 3 mM NADP and 3 mM P218 against MCSG1 screen condition G6 0.1 M sodium acetate pH 4.5, 25% PEG 3350 supplemented with 15% ethylene glycol as cryo-protectant, crystal tracking ID 292198g6, unique puck ID vsf3-2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→33.965 Å / Num. obs: 9854 / % possible obs: 97.5 % / Redundancy: 2.995 % / Biso Wilson estimate: 43.42 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.119 / Χ2: 0.899 / Net I/σ(I): 9.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.723.1320.5532.537420.8360.6799.7
2.72-2.793.1110.5062.817030.8670.61598.7
2.79-2.873.1110.423.317050.8930.50899.7
2.87-2.963.0780.3333.946570.8980.40498.9
2.96-3.063.0670.2654.946560.9560.32398.8
3.06-3.173.0450.1986.166240.970.24197.3
3.17-3.292.9720.1577.086040.980.19298.1
3.29-3.423.0140.148.315800.9810.1797.3
3.42-3.572.9640.1129.485600.9880.13797.7
3.57-3.752.9720.09111.235430.9880.11197.3
3.75-3.952.910.07512.524910.9950.09295.5
3.95-4.192.8740.06214.544670.9940.07696.3
4.19-4.482.9290.05515.314510.9940.06795.3
4.48-4.842.8960.04817.334120.9950.05896.7
4.84-5.32.8990.05715.543950.9950.0796.8
5.3-5.932.9360.05615.963460.990.0796.9
5.93-6.842.9090.05215.883190.9930.06495.2
6.84-8.382.8910.05118.392660.9930.06396.7
8.38-11.852.7810.04221.12100.9930.05396.8
11.85-33.9652.6830.04920.771230.9950.06189.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1df7

1df7


Resolution: 2.65→33.965 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.78
RfactorNum. reflection% reflection
Rfree0.2532 903 9.18 %
Rwork0.1974 --
obs0.2028 9837 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.52 Å2 / Biso mean: 47.3103 Å2 / Biso min: 17.89 Å2
Refinement stepCycle: final / Resolution: 2.65→33.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 148 48 2567
Biso mean--48.65 39.43 -
Num. residues----310
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1114X-RAY DIFFRACTION6.752TORSIONAL
12B1114X-RAY DIFFRACTION6.752TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6499-2.81590.34261470.29741491163899
2.8159-3.03320.3311390.25811509164899
3.0332-3.33820.29791300.23051504163498
3.3382-3.82060.2611520.21271459161197
3.8206-4.81140.21591730.15891454162796
4.8114-33.96780.22611620.15811517167996
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0355-0.48770.34662.6827-0.03351.8128-0.2576-0.30550.20580.55590.1582-0.0332-0.19990.14890.06760.40370.0620.00990.3751-0.09920.42828.8081-2.297517.7996
21.5736-0.10222.17843.59390.83137.0495-0.5151-1.1789-0.36020.57750.0969-0.04220.4671-0.28110.58430.50610.03680.07410.61140.02260.39428.3848-9.872425.9869
31.42220.41140.16343.5599-2.73475.6824-0.0598-0.43170.04390.00040.0351-0.07060.13460.6301-0.16030.2788-0.01760.07520.323-0.06720.327233.5426-10.77819.7155
43.9214-2.21461.44185.906-3.87583.05610.0125-0.0499-0.24920.4964-0.00180.3794-0.38610.250.00960.2799-00.01490.3344-0.0370.339523.2452-13.55293.5517
53.0947-0.33290.34591.39090.23773.5403-0.1376-0.4160.27620.16160.0547-0.3088-0.31560.04590.13560.28470.065-0.08530.3351-0.0640.514854.9442-14.488114.2869
60.62150.76781.83130.95872.31285.6429-0.1986-0.5817-0.01250.8434-0.1922-0.4480.05750.43460.18630.60510.0054-0.18520.8593-0.11480.869960.2949-12.987531.3004
74.34560.83022.32274.21511.44566.4982-0.2024-0.8147-0.24140.8778-0.3241-0.0680.7925-0.03250.00830.52730.0978-0.03420.56850.00920.419352.7832-21.78724.0833
82.47160.7254-0.21781.6429-0.35631.6516-0.1681-0.33410.00460.06780.1082-0.08670.0054-0.02140.07380.25740.0511-0.04370.3278-0.00830.512158.255-23.59145.4503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 77 )A2 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 94 )A78 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 128 )A95 - 128
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 156 )A129 - 156
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 66 )B2 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 77 )B67 - 77
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 94 )B78 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 156 )B95 - 156

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