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- PDB-7rzo: Crystal structure of a dihydrofolate reductase (folA) from Stenot... -

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Basic information

Entry
Database: PDB / ID: 7rzo
TitleCrystal structure of a dihydrofolate reductase (folA) from Stenotrophomonas maltophilia
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / SSGCID / folA / dihydrofolate reductase / DHFR / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
Dihydrofolate reductase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 dihydrofolate reductase from Stenotrophomonas maltophilia K279a
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4264
Polymers19,2671
Non-polymers1603
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.170, 104.170, 87.640
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-531-

HOH

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Components

#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 (strain K279a) (bacteria)
Strain: K279a / Gene: folA, Smlt0814 / Plasmid: StmaA.01062.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FPG1, dihydrofolate reductase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG-1 C7 (313874c7): 100 mM Tris:HCl, pH8.5, 200 mM CaCl2, 25% (w/v) PEG 4000: StmaA.01062.a.B1.PW38724 @ 26.35 mg/mL: 15% EG: puck/pin id: dqg0-6

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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 MX-300 / Detector: CCD / Date: Mar 5, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→37.66 Å / Num. obs: 22548 / % possible obs: 99.6 % / Redundancy: 9.788 % / Biso Wilson estimate: 32.421 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.057 / Χ2: 1.014 / Net I/σ(I): 24.88 / Num. measured all: 220707 / Scaling rejects: 12
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
1.8-1.859.90.564.2216147164416310.9320.5999.2
1.85-1.99.9360.4365.3815887161215990.9540.45999.2
1.9-1.959.9620.331715372155815430.9720.34999
1.95-2.019.8880.2529.3514901151515070.9810.26699.5
2.01-2.089.9170.19911.514618148014740.990.2199.6
2.08-2.159.930.15214.714021142014120.9920.1699.4
2.15-2.239.8920.12817.3713483136813630.9940.13599.6
2.23-2.329.8790.10420.7213248134713410.9960.1199.6
2.32-2.439.8530.09322.9312612128112800.9970.09899.9
2.43-2.559.8550.08126.0712013122312190.9980.08599.7
2.55-2.689.8720.0729.2511531116911680.9980.07399.9
2.68-2.859.7630.05934.1310876111511140.9980.06299.9
2.85-3.049.8020.0539.6110165103710370.9990.053100
3.04-3.299.6590.04345.294669819800.9990.04599.9
3.29-3.69.630.03651.8786679009000.9990.038100
3.6-4.029.5880.03355.2378818228220.9990.035100
4.02-4.659.5220.03257.269707327320.9990.034100
4.65-5.699.3820.03356.3459486356340.9990.03599.8
5.69-8.059.110.03454.3844914974930.9990.03699.2
8.05-37.668.060.03254.7924103052990.9980.03598

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hi6

5hi6


Resolution: 1.8→37.66 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 1998 8.86 %
Rwork0.1571 20546 -
obs0.1597 22544 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.16 Å2 / Biso mean: 30.5632 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 1.8→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 9 263 1551
Biso mean--38.98 41.67 -
Num. residues----164
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.28161380.24051432157099
1.84-1.890.24171420.20621456159899
1.89-1.950.23711380.17641429156799
1.95-2.010.17761440.17351429157399
2.01-2.090.20891360.17471462159899
2.09-2.170.21841270.160514571584100
2.17-2.270.18711390.162914601599100
2.27-2.390.20141450.16514431588100
2.39-2.540.21611480.164614651613100
2.54-2.730.19641540.170914571611100
2.73-3.010.19641580.159814591617100
3.01-3.440.16321490.151814841633100
3.44-4.340.1681300.126315281658100
4.34-37.660.16591500.15531585173599
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)
14.9892-4.2826-2.59753.54492.00216.42490.00450.187-0.2091-0.3464-0.0358-0.24020.14530.1540.15610.2148-0.05740.0390.1726-0.00850.216911.05646.581115.4247
23.87531.7279-0.77314.3045-1.58412.4573-0.0459-0.09620.1189-0.1989-0.1492-0.1225-0.23690.12750.28550.29520.0110.00030.1676-0.01180.24787.927821.551823.471
38.3379-6.3185-6.90335.34896.3388.2385-0.3935-0.5186-0.31040.59120.05820.18270.29230.23090.28890.2373-0.02030.00850.19190.07010.213610.09886.113828.0565
46.5461-2.2151.20883.19983.9388.1456-0.24210.19230.54570.20670.2557-0.7724-0.49790.3850.04910.2492-0.0373-0.00830.22760.0490.244821.686814.402420.928
54.8011-0.5554-0.5662.51132.19612.4191-0.0493-0.23340.09710.07070.1443-0.3687-0.32980.5285-0.06560.2304-0.03040.01020.23890.00190.223426.810710.379120.8168
66.7408-2.2794-1.6082.8679-2.24215.3063-0.1980.1566-0.3978-0.05770.04360.02330.52860.1480.15550.1811-0.02840.02570.1566-0.01780.219120.46642.152914.2105
76.0961.55652.40058.62545.20823.6713-0.29990.55540.2951-0.54670.2514-0.2519-0.51720.4876-0.02710.3012-0.0490.02660.25760.04970.20714.076913.08128.4651
82.91250.716-0.48146.27722.71474.4147-0.04960.09440.2374-0.18080.0230.0717-0.3863-0.10560.0280.19090.0042-0.02310.13820.0370.11915.452817.179318.3183
95.94942.3365-0.99765.91053.58356.6436-0.04140.38730.3778-0.52450.12380.50240.2218-0.2645-0.03180.13070.0226-0.04940.15040.01710.2121-0.63679.76813.4071
100.8828-0.7163-1.09016.93085.72594.531-0.0736-0.0672-0.02260.2506-0.13740.33590.2509-0.11480.21390.1932-0.02990.02030.1834-0.01180.19130.270711.87524.4178
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 51 )A40 - 51
5X-RAY DIFFRACTION5chain 'A' and (resid 52 through 79 )A52 - 79
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 100 )A80 - 100
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 110 )A101 - 110
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 129 )A111 - 129
9X-RAY DIFFRACTION9chain 'A' and (resid 130 through 145 )A130 - 145
10X-RAY DIFFRACTION10chain 'A' and (resid 146 through 163 )A146 - 163

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