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- PDB-3sa1: Bacuills anthracis Dihydrofolate Reductase bound propargyl-linked... -

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Basic information

Entry
Database: PDB / ID: 3sa1
TitleBacuills anthracis Dihydrofolate Reductase bound propargyl-linked TMP analog, UCP1021
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE
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-6DR / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsAnderson, A.C. / Beierlein, J.M.
CitationJournal: to be published
Title: SAR studies of heterocyclic propargyl-linked TMP analogs to Bacillus 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)41,4206
Polymers39,2152
Non-polymers2,2064
Water63135
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7103
Polymers19,6071
Non-polymers1,1032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7103
Polymers19,6071
Non-polymers1,1032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.094, 78.094, 67.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
11METMETASPASPAA1 - 104 - 13
21METMETASPASPBB1 - 104 - 13
12LEULEULEULEUAA25 - 2928 - 32
22LEULEULEULEUBB25 - 2928 - 32
13TYRTYRVALVALAA31 - 3234 - 35
23TYRTYRVALVALBB31 - 3234 - 35
14THRTHRTHRTHRAA35 - 3638 - 39
24THRTHRTHRTHRBB35 - 3638 - 39
15GLYGLYVALVALAA38 - 7141 - 74
25GLYGLYVALVALBB38 - 7141 - 74
16GLYGLYGLUGLUAA73 - 8176 - 84
26GLYGLYGLUGLUBB73 - 8176 - 84
17VALVALCYSCYSAA83 - 8786 - 90
27VALVALCYSCYSBB83 - 8786 - 90
18ASNASNGLUGLUAA89 - 9092 - 93
28ASNASNGLUGLUBB89 - 9092 - 93
19GLUGLUPROPROAA92 - 12895 - 131
29GLUGLUPROPROBB92 - 12895 - 131
110GLUGLUASPASPAA137 - 146140 - 149
210GLUGLUASPASPBB137 - 146140 - 149
111ASNASNLYSLYSAA149 - 160152 - 163
211ASNASNLYSLYSBB149 - 160152 - 163
112ASNASNTRPTRPAA20 - 2323 - 26
212ASNASNTRPTRPBB20 - 2323 - 26
113ASNASNASPASPAA12 - 1815 - 21
213ASNASNASPASPBB12 - 1815 - 21

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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-6DR / 6-ethyl-5-{3-[2-methoxy-5-(pyridin-4-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine


Mass: 359.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 52.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: initial crystal hits were grown in 27.5% (w/v) PEG 10,000, 0.1 M MES, pH 6.50, at an equal ratio of protein to crystallization solution. Microseeding was used to obtain isolated crystals in ...Details: initial crystal hits were grown in 27.5% (w/v) PEG 10,000, 0.1 M MES, pH 6.50, at an equal ratio of protein to crystallization solution. Microseeding was used to obtain isolated crystals in 10% (w/v) PEG 10,000 and 0.1 MES, pH 6.50 at a protein concentration of 5 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→42.63 Å / Num. all: 13990 / Num. obs: 13990 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Net I/σ(I): 5.2
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.4 / Num. unique all: 966 / Rsym value: 0.383 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.8Ldata scaling
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E0B

3e0b


Resolution: 2.5→42.63 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.46 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 699 5 %RANDOM
Rwork0.229 ---
all0.2304 13963 --
obs0.2304 13963 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.44 Å2 / Biso mean: 30.7904 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 150 35 2935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223011
X-RAY DIFFRACTIONr_angle_refined_deg1.3372.0024093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24224155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30615497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5011516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212320
X-RAY DIFFRACTIONr_mcbond_it0.5651.51646
X-RAY DIFFRACTIONr_mcangle_it1.07622678
X-RAY DIFFRACTIONr_scbond_it1.28131365
X-RAY DIFFRACTIONr_scangle_it2.1564.51412
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
555TIGHT POSITIONAL0.030.05
584LOOSE POSITIONAL0.045
555TIGHT THERMAL0.080.5
584LOOSE THERMAL0.0810
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 53 -
Rwork0.271 966 -
all-1019 -
obs-966 98.55 %

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