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- PDB-3tq8: Structure of the dihydrofolate reductase (folA) from Coxiella bur... -

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Basic information

Entry
Database: PDB / ID: 3tq8
TitleStructure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with trimethoprim
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / dihydrofolate reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic 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
Chem-NDP / TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFranklin, M.C. / Cassidy, M. / Hillerich, B. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Feb 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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)21,9603
Polymers20,9241
Non-polymers1,0362
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.340, 36.200, 53.810
Angle α, β, γ (deg.)90.00, 110.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrofolate reductase


Mass: 20924.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_1993, folA / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q83AB2, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O3 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 25% PEG 6000 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→26.44 Å / Num. all: 15111 / Num. obs: 14597 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.074 / Net I/σ(I): 15
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 8.8 / Rsym value: 0.132 / % possible all: 82.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unliganded CBU_1993

Resolution: 1.9→26.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.454 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23715 641 5.1 %RANDOM
Rwork0.18196 ---
obs0.18479 11999 85.19 %-
all-14837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.02 Å2
2---0.18 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 69 229 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221520
X-RAY DIFFRACTIONr_bond_other_d0.0010.021041
X-RAY DIFFRACTIONr_angle_refined_deg1.4352.0042064
X-RAY DIFFRACTIONr_angle_other_deg0.92232528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99523.52171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04615261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0461510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5071.5854
X-RAY DIFFRACTIONr_mcbond_other0.1241.5340
X-RAY DIFFRACTIONr_mcangle_it0.92721388
X-RAY DIFFRACTIONr_scbond_it1.4573666
X-RAY DIFFRACTIONr_scangle_it2.3534.5676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 25 -
Rwork0.386 460 -
obs--46.06 %
Refinement TLS params.Method: refined / Origin x: 13.9808 Å / Origin y: -0.7598 Å / Origin z: 10.4213 Å
111213212223313233
T0.0412 Å20.0108 Å20.0006 Å2-0.0161 Å20.0041 Å2--0.0143 Å2
L3.1735 °20.944 °20.5727 °2-2.2777 °20.6925 °2--2.0994 °2
S0.0841 Å °-0.0132 Å °-0.1667 Å °0.071 Å °-0.0128 Å °-0.0598 Å °0.077 Å °0.1213 Å °-0.0712 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 173
2X-RAY DIFFRACTION1A1001 - 2001
3X-RAY DIFFRACTION1A179 - 407

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