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

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Basic information

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


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FOLIC ACID / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)22,1113
Polymers20,9241
Non-polymers1,1872
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.154, 37.409, 52.943
Angle α, β, γ (deg.)90.00, 108.19, 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-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6

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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: 2.19 Å3/Da / Density % sol: 43.85 %
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: Oct 28, 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: 2.3→100 Å / Num. all: 8256 / Num. obs: 8168 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rsym value: 0.036 / Net I/σ(I): 30.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.429 / % possible all: 99.5

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Processing

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

Resolution: 2.4→14.19 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 31.123 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R: 0.752 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33343 337 5.1 %RANDOM
Rwork0.27302 ---
obs0.27587 6310 93.15 %-
all-7136 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.613 Å2
Baniso -1Baniso -2Baniso -3
1-10.54 Å20 Å22.39 Å2
2---3.61 Å20 Å2
3----5.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 80 0 1308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221341
X-RAY DIFFRACTIONr_bond_other_d0.0010.02924
X-RAY DIFFRACTIONr_angle_refined_deg1.0022.0351820
X-RAY DIFFRACTIONr_angle_other_deg0.80632250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.245149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64823.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.0515237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.685159
X-RAY DIFFRACTIONr_chiral_restr0.0520.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
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_it0.1151.5759
X-RAY DIFFRACTIONr_mcbond_other0.0161.5303
X-RAY DIFFRACTIONr_mcangle_it0.2121236
X-RAY DIFFRACTIONr_scbond_it0.2493582
X-RAY DIFFRACTIONr_scangle_it0.4224.5584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 20 -
Rwork0.385 407 -
obs--86.97 %
Refinement TLS params.Method: refined / Origin x: 14.6531 Å / Origin y: 0.6473 Å / Origin z: 11.0625 Å
111213212223313233
T0.1329 Å2-0.0503 Å20.0373 Å2-0.2512 Å2-0.08 Å2--0.1973 Å2
L5.8175 °20.4859 °2-1.8942 °2-5.1165 °22.0761 °2--8.8379 °2
S0.1519 Å °0.084 Å °-0.1593 Å °0.7057 Å °-0.701 Å °0.6225 Å °-0.0376 Å °-0.7282 Å °0.5491 Å °

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