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- PDB-7tj3: Crystal structure of a dihydrofolate reductase folA from Stenotro... -

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Basic information

Entry
Database: PDB / ID: 7tj3
TitleCrystal structure of a dihydrofolate reductase folA from Stenotrophomonas maltophilia bound to NADP and p218
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NIAID / structural genomics / DHFR / inhibitor / OXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia K279a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of a dihydrofolate reductase folA from Stenotrophomonas maltophilia bound to NADP and p218
Authors: Edwards, T.E. / deBouver, N.D. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5255
Polymers19,2671
Non-polymers1,2584
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.990, 101.990, 87.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-371-

HOH

21A-491-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate reductase


Mass: 19266.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria)
Strain: K279a / Gene: folA, Smlt0814 / Production host: Escherichia coli (E. coli) / References: UniProt: B2FPG1, dihydrofolate reductase

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Non-polymers , 5 types, 206 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: obtained synthetically / Formula: C18H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.95 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: StmaA.01062.a.B1.PW38724 at 19 mg/mL with 4 mM NADP and 4 mM p218 against MCSG1 screen condition B5, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 25 % PEG 3350 supplemented with 20% ethylene glycol as ...Details: StmaA.01062.a.B1.PW38724 at 19 mg/mL with 4 mM NADP and 4 mM p218 against MCSG1 screen condition B5, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 25 % PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 323617b5, unique puck ID wrq8-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→36.06 Å / Num. obs: 33598 / % possible obs: 100 % / Redundancy: 10.543 % / Biso Wilson estimate: 20.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.057 / Χ2: 0.93 / Net I/σ(I): 24.06 / Num. measured all: 354215
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.5910.2570.6023.825294246624660.9140.633100
1.59-1.6310.60.4814.8924995235823580.9360.505100
1.63-1.6810.5790.3696.2424723233723370.9630.388100
1.68-1.7310.6540.2997.7323939224722470.9780.314100
1.73-1.7910.6640.22210.2723643221722170.9870.233100
1.79-1.8510.6410.1613.7322495211421140.9940.168100
1.85-1.9210.6640.12517.3321894205320530.9960.132100
1.92-210.6840.09821.9921090197419740.9970.103100
2-2.0910.6640.08125.820165189118910.9970.085100
2.09-2.1910.6230.06730.3619333182018200.9980.071100
2.19-2.3110.6550.0633.6318443173117310.9980.063100
2.31-2.4510.6280.05436.4917473164416440.9990.057100
2.45-2.6210.620.05239.0616536155715570.9980.055100
2.62-2.8310.5560.04941.6215359145514550.9990.051100
2.83-3.110.540.04445.9414060133413340.9990.046100
3.1-3.4710.4570.04248.8212737121912180.9990.04499.9
3.47-410.3580.0450.5311270108810880.9990.043100
4-4.910.2860.04151.7294949249230.9980.04499.9
4.9-6.9310.0840.04150.0274327397370.9980.04499.7
6.93-36.068.8480.04547.6238404424340.9960.04998.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.20-4438refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7rzo

7rzo


Resolution: 1.55→36.06 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 1988 5.92 %
Rwork0.1645 31609 -
obs0.1655 33597 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.82 Å2 / Biso mean: 26.3933 Å2 / Biso min: 13.04 Å2
Refinement stepCycle: final / Resolution: 1.55→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 84 203 1566
Biso mean--29.97 37.81 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.55-1.590.23961440.206622182362
1.59-1.630.22311280.192922272355
1.63-1.680.22941540.200722402394
1.68-1.730.23041270.206622172344
1.73-1.80.21771640.185422222386
1.8-1.870.20181170.169922512368
1.87-1.950.18811570.159422172374
1.95-2.060.18041440.166622472391
2.06-2.180.22051400.163422412381
2.19-2.350.17371510.15522522403
2.35-2.590.17231360.161922652401
2.59-2.960.17731310.17722812412
2.96-3.730.17871420.152123222464
3.74-36.060.15631530.15824092562
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)
16.8851-3.18722.06747.7006-1.15585.24730.01780.17980.1953-0.5743-0.00550.2921-0.012-0.2883-0.11060.1126-0.0365-0.01780.1274-0.01620.1281-9.8326-5.9615-28.0858
22.62131.20360.3223.02950.85166.92140.0062-0.0097-0.23340.09070.02950.07060.5108-0.1143-0.03260.2181-0.0066-0.02130.10010.02560.209-7.179-21.94-19.633
35.4446-4.74844.25888.6767-5.58527.3056-0.288-0.42490.11150.55180.1056-0.0877-0.2258-0.23530.16660.2147-0.00810.00170.1942-0.03620.1806-8.7155-6.9946-14.7048
44.0986-1.171-1.37973.7795-2.17573.9158-0.0915-0.1526-0.2095-0.01890.05090.17090.1616-0.17360.08280.1217-0.018-0.01020.1741-0.02120.1628-20.8653-11.3776-20.9354
53.56420.62030.31543.5073-1.99533.0538-0.03790.1591-0.25310.00430.22970.42970.4095-0.8175-0.16560.1638-0.0368-0.01680.2879-0.02690.2291-28.4727-11.6422-25.1311
64.4825-2.73331.14584.8335-2.63453.3202-0.07420.15410.37840.0682-0.0463-0.0273-0.1628-0.1080.10330.1507-0.0082-0.01750.1756-0.01640.199-18.5978-2.0149-28.918
72.4575-0.06011.03954.547-1.19183.34530.05950.1215-0.1882-0.19440.00820.05840.325-0.0448-0.07540.1138-0.00980.02030.1078-0.03150.1125-7.5466-15.8989-28.9764
81.34250.54640.09062.5451-0.62810.1943-0.00250.0414-0.08250.1197-0.1226-0.3432-0.11240.13560.05820.1892-0.0171-0.00590.178-0.00120.20911.8938-12.7476-21.3241
96.3439-1.12322.40335.66730.02393.30250.05910.3917-0.0384-0.4921-0.0395-0.1555-0.13840.4395-0.00060.1504-0.02070.02490.11380.0070.15360.8963-8.1592-27.1905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 9 )A0 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 25 )A10 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 39 )A26 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 63 )A40 - 63
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 79 )A64 - 79
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 100 )A80 - 100
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 129 )A101 - 129
8X-RAY DIFFRACTION8chain 'A' and (resid 130 through 154 )A130 - 154
9X-RAY DIFFRACTION9chain 'A' and (resid 155 through 163 )A155 - 163

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