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

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Basic information

Entry
Database: PDB / ID: 3tqa
TitleStructure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with NADPH
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductase
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
Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)21,6702
Polymers20,9241
Non-polymers7451
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)49.419, 37.026, 52.989
Angle α, β, γ (deg.)90.00, 108.02, 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

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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: 2.23 Å3/Da / Density % sol: 44.82 %
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: 8034 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rsym value: 0.062 / Net I/σ(I): 20.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.558 / % possible all: 99.8

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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: 2.3→25.77 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 22.644 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.456 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29854 407 5.1 %RANDOM
Rwork0.24715 ---
obs0.24965 7561 96.27 %-
all-8277 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.41 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å20 Å20.15 Å2
2---1.32 Å20 Å2
3----3.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 48 0 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221372
X-RAY DIFFRACTIONr_bond_other_d0.0010.02958
X-RAY DIFFRACTIONr_angle_refined_deg1.012.0091863
X-RAY DIFFRACTIONr_angle_other_deg0.81132333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1325156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49123.60761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.58815245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7141510
X-RAY DIFFRACTIONr_chiral_restr0.0540.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211443
X-RAY DIFFRACTIONr_gen_planes_other00.02273
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_it0.1111.5790
X-RAY DIFFRACTIONr_mcbond_other0.0131.5313
X-RAY DIFFRACTIONr_mcangle_it0.20721287
X-RAY DIFFRACTIONr_scbond_it0.2543582
X-RAY DIFFRACTIONr_scangle_it0.4774.5576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.7 21 -
Rwork0.567 415 -
obs--73.77 %
Refinement TLS params.Method: refined / Origin x: 14.4271 Å / Origin y: 0.8398 Å / Origin z: 11.8337 Å
111213212223313233
T0.328 Å20.0045 Å20.0077 Å2-0.1745 Å2-0.0658 Å2--0.0457 Å2
L9.5299 °20.9307 °2-1.2311 °2-6.0974 °22.1853 °2--6.9729 °2
S0.384 Å °-0.2522 Å °-0.0377 Å °0.3043 Å °-0.817 Å °0.4134 Å °-0.2012 Å °-0.7521 Å °0.4331 Å °

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