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- PDB-3fl8: Crystal structure of B. anthracis dihydrofolate reductase (DHFR) ... -

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Basic information

Entry
Database: PDB / ID: 3fl8
TitleCrystal structure of B. anthracis dihydrofolate reductase (DHFR) with RAB1, a TMP-dihydrophthalazine derivative
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / PYRIMIDINE / DIHYDROPHTHALAZINE
Function / homology
Function and homology information


glycine biosynthetic process / 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-RAR / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2881 Å
AuthorsBourne, C.R. / Barrow, W.W.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2009
Title: Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity.
Authors: Bourne, C.R. / Bunce, R.A. / Bourne, P.C. / Berlin, K.D. / Barrow, E.W. / Barrow, W.W.
History
DepositionDec 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_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
C: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
F: Dihydrofolate reductase
G: Dihydrofolate reductase
H: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,13724
Polymers156,9248
Non-polymers4,21316
Water27,4011521
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1423
Polymers19,6151
Non-polymers5272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.178, 135.920, 168.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPROPROAA2 - 1502 - 150
21ILEILEPROPROBB2 - 1502 - 150
31ILEILEPROPROCC2 - 1502 - 150
41ILEILEPROPRODD2 - 1502 - 150
51ILEILEPROPROEE2 - 1502 - 150
61ILEILEPROPROFF2 - 1502 - 150
71ILEILEPROPROGG2 - 1502 - 150
81ILEILEASNASNHH2 - 662 - 66
82CYSCYSCYSCYSHH74 - 8774 - 87
83GLUGLUPROPROHH90 - 15090 - 150

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Components

#1: Protein
Dihydrofolate reductase /


Mass: 19615.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS2083, BA_2237, dfrA, DHFR, GBAA2237 / Plasmid: pCRT7/C-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81R22, dihydrofolate reductase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-RAR / 5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1-propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine-2,4-diamine / (S)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-propylphthalazin-2(1H)-yl)prop-2-en-1-one


Mass: 486.566 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H30N6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1521 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 12% PEG 3350, 0.2M CaCl2, 0.1M MES, 3% glycerol, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 22, 2008 / Details: Montel multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.288→25 Å / Num. all: 71501 / Num. obs: 69571 / % possible obs: 97.3 % / Redundancy: 13.7 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.123 / Net I/σ(I): 16.1
Reflection shellResolution: 2.288→2.4 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 8056 / Rsym value: 0.476 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QK8

2qk8


Resolution: 2.2881→24.972 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3513 5.05 %random
Rwork0.206 66058 --
obs0.209 69571 97.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.106 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 96.56 Å2 / Biso mean: 29.282 Å2 / Biso min: 5.08 Å2
Baniso -1Baniso -2Baniso -3
1-5.921 Å20 Å2-0 Å2
2--1.876 Å20 Å2
3----7.797 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.2881→24.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10791 0 296 1521 12608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711400
X-RAY DIFFRACTIONf_angle_d1.05115447
X-RAY DIFFRACTIONf_chiral_restr0.0641579
X-RAY DIFFRACTIONf_plane_restr0.0061963
X-RAY DIFFRACTIONf_dihedral_angle_d15.8194184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1194X-RAY DIFFRACTIONPOSITIONAL
12B1194X-RAY DIFFRACTIONPOSITIONAL0.04
13C1203X-RAY DIFFRACTIONPOSITIONAL0.049
14D1168X-RAY DIFFRACTIONPOSITIONAL0.051
15E1194X-RAY DIFFRACTIONPOSITIONAL0.042
16F1176X-RAY DIFFRACTIONPOSITIONAL0.044
17G1185X-RAY DIFFRACTIONPOSITIONAL0.042
18H1044X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2881-2.31940.31221080.26682045X-RAY DIFFRACTION77
2.3194-2.35250.3211400.24792595X-RAY DIFFRACTION96
2.3525-2.38760.31851430.2392543X-RAY DIFFRACTION96
2.3876-2.42490.33561230.23362618X-RAY DIFFRACTION96
2.4249-2.46460.27971300.23212600X-RAY DIFFRACTION97
2.4646-2.50710.27581390.22772580X-RAY DIFFRACTION97
2.5071-2.55260.30891480.23832628X-RAY DIFFRACTION98
2.5526-2.60170.30121180.24662641X-RAY DIFFRACTION98
2.6017-2.65470.32751520.24032594X-RAY DIFFRACTION98
2.6547-2.71240.30761590.23152647X-RAY DIFFRACTION98
2.7124-2.77540.29631510.2192622X-RAY DIFFRACTION98
2.7754-2.84470.29121270.22142688X-RAY DIFFRACTION99
2.8447-2.92150.27321480.21652633X-RAY DIFFRACTION99
2.9215-3.00740.27981310.21942680X-RAY DIFFRACTION99
3.0074-3.10430.25351320.20742715X-RAY DIFFRACTION99
3.1043-3.2150.25621340.20512636X-RAY DIFFRACTION99
3.215-3.34340.26161560.20112665X-RAY DIFFRACTION99
3.3434-3.49520.24731420.19712695X-RAY DIFFRACTION99
3.4952-3.67890.2331260.18672697X-RAY DIFFRACTION99
3.6789-3.90860.20741480.17692697X-RAY DIFFRACTION99
3.9086-4.20910.1991430.15932714X-RAY DIFFRACTION99
4.2091-4.63020.18331480.15112739X-RAY DIFFRACTION100
4.6302-5.29470.17361640.14332746X-RAY DIFFRACTION100
5.2947-6.64980.20421570.17392785X-RAY DIFFRACTION100
6.6498-24.9740.19921460.19052855X-RAY DIFFRACTION97

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