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- PDB-3s9u: Bacillus anthracis Dihydrofolate Reductase bound to propargyl-lin... -

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Basic information

Entry
Database: PDB / ID: 3s9u
TitleBacillus anthracis Dihydrofolate Reductase bound to propargyl-linked TMP analog, UCP120J
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE
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-5DR / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAnderson, A.C. / Beierlein, J.M.
CitationJournal: To be Published
Title: Structure-Activity Studies of Heterocyclic Propargyl-linked TMP Analogs Targeting Bacillus anthracis Dihydrofolate Reductase
Authors: Anderson, A.C. / Beierlein, J.M. / Viswanathan, K. / Wright, D.L.
History
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)41,4186
Polymers39,2152
Non-polymers2,2044
Water5,116284
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7093
Polymers19,6071
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7093
Polymers19,6071
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.187, 78.187, 67.094
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:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 294 - 32
21METMETLEULEUBB1 - 294 - 32
12TYRTYRTHRTHRAA31 - 3634 - 39
22TYRTYRTHRTHRBB31 - 3634 - 39
13GLYGLYGLUGLUAA38 - 9041 - 93
23GLYGLYGLUGLUBB38 - 9041 - 93
14GLUGLUTYRTYRAA92 - 10895 - 111
24GLUGLUTYRTYRBB92 - 10895 - 111
15ASPASPGLUGLUAA110 - 129113 - 132
25ASPASPGLUGLUBB110 - 129113 - 132
16VALVALASPASPAA138 - 146141 - 149
26VALVALASPASPBB138 - 146141 - 149
17LYSLYSGLUGLUAA148 - 159151 - 162
27LYSLYSGLUGLUBB148 - 159151 - 162

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Components

#1: Protein Dihydrofolate reductase


Mass: 19607.330 Da / Num. of mol.: 2 / Mutation: I2R
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-5DR / 6-ethyl-5-[3-(4-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-2,4-diamine


Mass: 358.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: initial hits were grown at room temperature by hanging drop diffusion in 21.0% (w/v) PEG 10,000, 0.1 M MES, pH 6.75, at an equal ratio of protein to crystallization solution. Microseeding ...Details: initial hits were grown at room temperature by hanging drop diffusion in 21.0% (w/v) PEG 10,000, 0.1 M MES, pH 6.75, at an equal ratio of protein to crystallization solution. Microseeding was used to obtain isolated crystals in 11% PEG 10,000 and 0.1 MES, pH 6.75 at a protein concentration of 8 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979505 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979505 Å / Relative weight: 1
ReflectionResolution: 1.9→30.83 Å / Num. all: 30364 / Num. obs: 30364 / % possible obs: 99.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7.4 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 25.6
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2228 / Rsym value: 0.397 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E0B

3e0b


Resolution: 1.9→30.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.08 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22311 1619 5.1 %RANDOM
Rwork0.18998 ---
all0.22311 3096 --
obs0.19161 30364 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.748 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 150 284 3194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223118
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9994249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5265352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59424.161161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91315520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0031516
X-RAY DIFFRACTIONr_chiral_restr0.0760.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212434
X-RAY DIFFRACTIONr_mcbond_it0.4961.51714
X-RAY DIFFRACTIONr_mcangle_it0.9422801
X-RAY DIFFRACTIONr_scbond_it1.08531404
X-RAY DIFFRACTIONr_scangle_it1.8734.51448
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A576tight positional0.020.05
B618loose positional0.025
A576tight thermal0.060.5
B618loose thermal0.0510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 116 -
Rwork0.251 2228 -
obs--99.91 %

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