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

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Basic information

Entry
Database: PDB / ID: 3jwk
TitleCrystal structure of Bacillus anthracis (Y102F) dihydrofolate reductase complexed with NADPH and (S)-2,4-diamino-5-(3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-methylpyrimidine (UCP114A)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding
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-5WB / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsAnderson, A.C. / Beierlein, J.M. / Karri, N.G.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Targeted Mutations in Bacillus anthracis Dihydrofolate Reductase Condense Complex Structure-Activity Relationships
Authors: Beierlein, J.M. / Karri, N.G. / Anderson, A.C.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,2196
Polymers40,0122
Non-polymers2,2084
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.858, 77.858, 67.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

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-5WB / 5-[(3S)-3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine / (S)-2,4-diamino-5-(3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-methylpyrimidine


Mass: 358.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
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, 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: X25 / Wavelength: 0.9966 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9966 Å / Relative weight: 1
ReflectionResolution: 2.08→42.68 Å / Num. all: 23117 / Num. obs: 23117 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 26.1
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1697 / Rsym value: 0.463 / % possible all: 100

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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: 2.08→42.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.166 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21293 1240 5.1 %RANDOM
Rwork0.18299 ---
all0.18453 23117 --
obs0.18453 23117 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.08→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 148 261 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.39824089
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85923.974156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87915495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3251516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.21301
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21997
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.51711
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12922680
X-RAY DIFFRACTIONr_scbond_it1.65931558
X-RAY DIFFRACTIONr_scangle_it2.4124.51407
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
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
657tight positional0.040.05
703loose positional0.435
657tight thermal0.120.5
703loose thermal110
LS refinement shellResolution: 2.08→2.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 86 -
Rwork0.194 1697 -
obs-1697 100 %

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