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- PDB-3jw5: Crystal structure of Bacillus anthracis (Y102F) dihydrofolate red... -

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Basic information

Entry
Database: PDB / ID: 3jw5
TitleCrystal structure of Bacillus anthracis (Y102F) dihydrofolate reductase complexed with NADPH and Trimethoprim
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 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 / metal ion 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 / TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsAnderson, A.C. / Beierlein, J.M. / Karri, N.G.
CitationJournal: To be Published
Title: Mutational Studies into Trimethoprim Resistance in Bacillus anthracis Dihydrofolate Reductase
Authors: Beierlein, J.M. / Karri, N.G. / Anderson, A.C.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0836
Polymers40,0122
Non-polymers2,0714
Water64936
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0423
Polymers20,0061
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0423
Polymers20,0061
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.991, 74.991, 67.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 3 / Auth seq-ID: -2 - 162 / Label seq-ID: 4 - 168

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dihydrofolate reductase


Mass: 20005.771 Da / Num. of mol.: 2 / Mutation: I2R, Y102F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS2083, BA_2237, dfrA, GBAA2237, GBAA_2237 / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q81R22, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N4O3 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: Initially grown in 25% PEG 10000, 0.1 M MES. Macroseeding in 10% PEG 10000, 0.1 M MES. Trimethoprim soaked into seeds, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.89→37.5 Å / Num. all: 7952 / Num. obs: 7952 / % possible obs: 98.16 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.179 / Rsym value: 0.179 / Net I/σ(I): 11.6
Reflection shellResolution: 2.89→2.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.3 / Num. unique all: 520 / Rsym value: 0.443 / % possible all: 85.98

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EOB

3eob


Resolution: 2.89→37.5 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.863 / SU B: 19.268 / SU ML: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26047 389 4.7 %RANDOM
Rwork0.21196 ---
all0.21422 7952 --
obs0.21422 7952 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.89→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 138 36 2932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222995
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9934067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02123.806155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87415495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0861517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022299
X-RAY DIFFRACTIONr_nbd_refined0.1980.21411
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.27
X-RAY DIFFRACTIONr_mcbond_it0.41.51682
X-RAY DIFFRACTIONr_mcangle_it0.73122674
X-RAY DIFFRACTIONr_scbond_it0.7331512
X-RAY DIFFRACTIONr_scangle_it1.2484.51392
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
659tight positional0.040.05
712loose positional0.555
659tight thermal0.040.5
712loose thermal0.6810
LS refinement shellResolution: 2.89→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 32 -
Rwork0.278 520 -
obs-520 85.98 %

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