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- PDB-3ro9: Candida glabrata dihydrofolate reductase complexed with NADPH and... -

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Basic information

Entry
Database: PDB / ID: 3ro9
TitleCandida glabrata dihydrofolate reductase complexed with NADPH and 6-ethyl-5-[(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP1006)
ComponentsStrain CBS138 chromosome J complete sequence
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Antifungal Agents / Candida glabrata / Drug Design / Enzyme Inhibitors / Fungal Proteins / Models / Molecular Structure / Structure-Activity Relationship / Tetrahydrofolate Dehydrogenase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP 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-06U / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.596 Å
AuthorsPaulsen, J.L. / Anderson, A.C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Structural analysis of the active sites of dihydrofolate reductase from two species of Candida uncovers ligand-induced conformational changes shared among species.
Authors: Paulsen, J.L. / Viswanathan, K. / Wright, D.L. / Anderson, A.C.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 28, 2024Group: 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 / 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.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: Strain CBS138 chromosome J complete sequence
B: Strain CBS138 chromosome J complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6566
Polymers52,4182
Non-polymers2,2384
Water64936
1
A: Strain CBS138 chromosome J complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3283
Polymers26,2091
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Strain CBS138 chromosome J complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3283
Polymers26,2091
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.260, 42.260, 238.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: 06U / Beg label comp-ID: 06U / End auth comp-ID: HIS / End label comp-ID: HIS / End label seq-ID: 225 / Refine code: 2 / Auth seq-ID: 1 - 227

Dom-IDAuth asym-IDLabel asym-ID
1AD - A
2BF - B

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Components

#1: Protein Strain CBS138 chromosome J complete sequence


Mass: 26209.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0J03894g, DHFR / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FPH0
#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-06U / 6-ethyl-5-{(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine


Mass: 373.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2010 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.596→41.63 Å / Num. all: 10629 / Num. obs: 10629 / % possible obs: 90.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3 % / Rmerge(I) obs: 0.051 / Χ2: 2.795 / Net I/σ(I): 21.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.596-2.673.20.1376122.63695.9
2.67-2.713.30.1315642.71996.1
2.71-2.773.20.1175752.79294.9
2.77-2.823.20.1096162.77395.5
2.82-2.883.10.1035812.78794.9
2.88-2.953.10.0895563.06695
2.95-3.0230.0886033.06993.2
3.02-3.1130.0795522.90492.8
3.11-3.22.90.0735533.42889.5
3.2-3.32.90.0675773.06691
3.3-3.422.90.0645393.23290.6
3.42-3.562.70.0535693.00187.4
3.56-3.722.70.0465163.13189.4
3.72-3.912.70.0475422.82485.6
3.91-4.162.70.0474952.97581.7
4.16-4.482.60.0415213.17284.3
4.48-4.932.70.0375202.51783.7
4.93-5.642.90.045512.51787.5
5.64-7.113.30.0385602.11688.6
7.11-504.40.0375822.10790.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.596→41.63 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 13.018 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 548 4.9 %RANDOM
Rwork0.2018 ---
obs0.2049 10629 87.05 %-
all-10629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.54 Å2 / Biso mean: 31.7562 Å2 / Biso min: 4.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.596→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 152 36 3880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223946
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9995354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5485448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.82524.086186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39315694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2651524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022954
X-RAY DIFFRACTIONr_nbd_refined0.2180.21630
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22628
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2147
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.212
X-RAY DIFFRACTIONr_mcbond_it0.5331.52324
X-RAY DIFFRACTIONr_mcangle_it0.92723646
X-RAY DIFFRACTIONr_scbond_it1.17431910
X-RAY DIFFRACTIONr_scangle_it1.9084.51708
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
900TIGHT POSITIONAL0.020.05
946MEDIUM POSITIONAL0.30.5
900TIGHT THERMAL0.040.5
946MEDIUM THERMAL0.262
LS refinement shellResolution: 2.596→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 28 -
Rwork0.266 414 -
all-442 -
obs--48.04 %

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