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

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Basic information

Entry
Database: PDB / ID: 3qly
TitleCandida glabrata dihydrofolate reductase complexed with NADPH and 6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP115A)
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-55V / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.519 Å
AuthorsPaulsen, J.L. / Bendel, S.D. / Anderson, A.C.
CitationJournal: Chem.Biol.Drug Des. / Year: 2011
Title: Crystal Structures of Candida albicans Dihydrofolate Reductase Bound to Propargyl-Linked Antifolates Reveal the Flexibility of Active Site Loop Residues Critical for Ligand Potency and Selectivity.
Authors: Paulsen, J.L. / Bendel, S.D. / Anderson, A.C.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Sep 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_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_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)55,0586
Polymers52,8552
Non-polymers2,2044
Water73941
1
A: Strain CBS138 chromosome J complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5293
Polymers26,4271
Non-polymers1,1022
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)27,5293
Polymers26,4271
Non-polymers1,1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.731, 42.731, 230.839
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
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B1 - 227
2111A1 - 227

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Components

#1: Protein Strain CBS138 chromosome J complete sequence


Mass: 26427.334 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-55V / 6-methyl-5-[3-methyl-3-(3,4,5-trimethoxyphenyl)but-1-yn-1-yl]pyrimidine-2,4-diamine / 2,4-Diamino-5-[3-(3,4,5-trimethoxyphenyl)pent-1-ynyl]-6-methylpyrimidine


Mass: 356.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl2, 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 3, 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: 2.519→50 Å / Num. all: 13749 / Num. obs: 13749 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.108 / Χ2: 1.847 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.519-2.655.10.41313521.1771100
2.65-2.765.30.38813771.2081100
2.76-2.885.40.30613931.2691100
2.88-3.045.40.23513771.3961100
3.04-3.235.40.1813651.6291100
3.23-3.475.40.14713751.841100
3.47-3.825.40.10313942.2861100
3.82-4.385.30.08313962.8531100
4.38-5.515.20.06813802.8341100
5.51-505.30.04614091.96199.5

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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
Starting model: PDB ENTRY 3CSE

3cse


Resolution: 2.519→30.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 10.776 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 690 5 %RANDOM
Rwork0.2108 ---
all0.2136 13749 --
obs0.2136 13749 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.47 Å2 / Biso mean: 30.9484 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.519→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 148 41 3881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0223940
X-RAY DIFFRACTIONr_angle_refined_deg0.6971.9995350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1715448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94424.086186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51615694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9991524
X-RAY DIFFRACTIONr_chiral_restr0.0580.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022942
X-RAY DIFFRACTIONr_nbd_refined0.2260.21704
X-RAY DIFFRACTIONr_nbtor_refined0.320.22622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0650.212
X-RAY DIFFRACTIONr_mcbond_it0.5621.52305
X-RAY DIFFRACTIONr_mcangle_it0.97623646
X-RAY DIFFRACTIONr_scbond_it1.32231906
X-RAY DIFFRACTIONr_scangle_it2.1224.51704
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 1846 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.030.05
TIGHT THERMAL0.040.5
LS refinement shellResolution: 2.519→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 42 -
Rwork0.243 799 -
all-841 -
obs--87.6 %

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