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- PDB-8sze: Crystal structure of Yersinia pestis dihydrofolate reductase in c... -

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Basic information

Entry
Database: PDB / ID: 8sze
TitleCrystal structure of Yersinia pestis dihydrofolate reductase in complex with Trimethoprim
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShaw, G.X. / Cherry, S. / Tropea, J.E. / Waugh, D.S. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To be published
Title: Crystal structure of Yersinia pestis dihydrofolate reductase in complex with Trimethoprim
Authors: Shaw, G.X. / Cherry, S. / Tropea, J.E. / Waugh, D.S. / Ji, X.
History
DepositionMay 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)38,13016
Polymers36,6732
Non-polymers1,45714
Water1,38777
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0849
Polymers18,3371
Non-polymers7478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0477
Polymers18,3371
Non-polymers7106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.421, 115.421, 146.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase


Mass: 18336.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: folA, tmrA, YPO0486 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N4BLI0, dihydrofolate reductase

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Non-polymers , 5 types, 91 molecules

#2: Chemical ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium sulfate, isoproponal

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2006 / Details: Double crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→30 Å / Num. obs: 20235 / % possible obs: 96.5 % / Redundancy: 13.4 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.03 / Rrim(I) all: 0.12 / Χ2: 0.994 / Net I/σ(I): 9.8 / Num. measured all: 270357
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.48-2.574.20.82514500.5740.8540.4120.9310.95271
2.57-2.676.30.8519480.6460.8860.3420.9220.99695.4
2.67-2.798.80.7920090.8410.9560.2680.8370.99698.1
2.79-2.9412.20.72820530.8860.9690.2030.7581.00399.6
2.94-3.1215.10.58620640.9750.9940.1420.6040.943100
3.12-3.3615.90.30920670.990.9970.0730.3181.04100
3.36-3.716.20.15320990.9960.9990.0370.1581.014100
3.7-4.2417.10.08221000.99910.020.0841.002100
4.24-5.3317.60.05221450.99910.0120.0530.975100
5.33-3016.50.04123000.99910.010.0420.988100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.87 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 1997 9.9 %Random selection
Rwork0.2151 ---
obs0.2175 20173 98.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 85 77 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042514
X-RAY DIFFRACTIONf_angle_d0.6023404
X-RAY DIFFRACTIONf_dihedral_angle_d18.481901
X-RAY DIFFRACTIONf_chiral_restr0.06355
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.33221240.33281115X-RAY DIFFRACTION86
2.56-2.630.33361320.30361214X-RAY DIFFRACTION94
2.63-2.710.32741360.28471242X-RAY DIFFRACTION97
2.71-2.80.30621390.25541268X-RAY DIFFRACTION98
2.8-2.90.29621420.24761286X-RAY DIFFRACTION99
2.9-3.010.30451420.24661289X-RAY DIFFRACTION100
3.01-3.150.28271440.25761321X-RAY DIFFRACTION100
3.15-3.310.26341430.23961296X-RAY DIFFRACTION100
3.32-3.520.25251450.21011319X-RAY DIFFRACTION100
3.52-3.790.22611440.20421314X-RAY DIFFRACTION100
3.79-4.170.22751470.19611331X-RAY DIFFRACTION100
4.18-4.780.17711480.16131349X-RAY DIFFRACTION100
4.78-6.010.21851490.19091361X-RAY DIFFRACTION100
6.01-29.870.21711620.21891471X-RAY DIFFRACTION100

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