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- PDB-3sai: Bacuills anthracis Dihydrofolate Reductase bound to propargyl-lin... -

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Basic information

Entry
Database: PDB / ID: 3sai
TitleBacuills anthracis Dihydrofolate Reductase bound to propargyl-linked TMP analog, UCP1015
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-9DR / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAnderson, A.C. / Beierlein, J.M.
CitationJournal: To be Published
Title: SAR studies of heterocyclic propargyl-linked TMP analogs targeting 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,90311
Polymers39,2152
Non-polymers2,6899
Water4,125229
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0877
Polymers19,6071
Non-polymers1,4806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8164
Polymers19,6071
Non-polymers1,2093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.880, 77.880, 67.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-292-

HOH

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
11VALVALASPASPAA3 - 106 - 13
21VALVALASPASPBB3 - 106 - 13
12ASNASNGLYGLYAA12 - 1615 - 19
22ASNASNGLYGLYBB12 - 1615 - 19
13ASPASPTRPTRPAA18 - 2321 - 26
23ASPASPTRPTRPBB18 - 2321 - 26
14LEULEUGLUGLUAA25 - 2828 - 31
24LEULEUGLUGLUBB25 - 2828 - 31
15TYRTYRVALVALAA31 - 3234 - 35
25TYRTYRVALVALBB31 - 3234 - 35
16THRTHRTHRTHRAA35 - 3638 - 39
26THRTHRTHRTHRBB35 - 3638 - 39
17GLYGLYVALVALAA38 - 7141 - 74
27GLYGLYVALVALBB38 - 7141 - 74
18GLYGLYLEULEUAA73 - 8676 - 89
28GLYGLYLEULEUBB73 - 8676 - 89
19ASNASNGLUGLUAA89 - 9092 - 93
29ASNASNGLUGLUBB89 - 9092 - 93
110GLUGLUGLUGLUAA92 - 12995 - 132
210GLUGLUGLUGLUBB92 - 12995 - 132
111GLUGLUVALVALAA137 - 140140 - 143
211GLUGLUVALVALBB137 - 140140 - 143
112LYSLYSASPASPAA142 - 146145 - 149
212LYSLYSASPASPBB142 - 146145 - 149
113ASNASNGLUGLUAA149 - 159152 - 162
213ASNASNGLUGLUBB149 - 159152 - 162

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 238 molecules

#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-9DR / 6-ethyl-5-{3-[3-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: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
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 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→42.56 Å / Num. obs: 19019 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.15 % / Rmerge(I) obs: 0.096 / Rsym value: 0.115 / Net I/σ(I): 6.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2 / Num. unique all: 1300 / Rsym value: 0.433 / % possible all: 98.2

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Processing

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

3e0b


Resolution: 2.25→42.56 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.643 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 979 5.2 %RANDOM
Rwork0.2089 ---
all0.2111 19001 --
obs0.2111 19001 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.1 Å2 / Biso mean: 27.9772 Å2 / Biso min: 16.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 179 229 3168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223096
X-RAY DIFFRACTIONr_angle_refined_deg1.2032.0054205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63624.074162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93915514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.171517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212383
X-RAY DIFFRACTIONr_mcbond_it0.481.51672
X-RAY DIFFRACTIONr_mcangle_it0.922728
X-RAY DIFFRACTIONr_scbond_it1.07631424
X-RAY DIFFRACTIONr_scangle_it1.7944.51467
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
538TIGHT POSITIONAL0.030.05
561LOOSE POSITIONAL0.035
538TIGHT THERMAL0.070.5
561LOOSE THERMAL0.0610
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 72 -
Rwork0.283 1300 -
all-1372 -
obs-1300 97.72 %

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