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- PDB-5ujx: Crystal structure of DHFR in 20% Isopropanol -

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Basic information

Entry
Database: PDB / ID: 5ujx
TitleCrystal structure of DHFR in 20% Isopropanol
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dynamics
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / 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
FOLIC ACID / ISOPROPYL ALCOHOL / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCuneo, M.J. / Agarwal, P.K.
CitationJournal: Biochemistry / Year: 2018
Title: Modulating Enzyme Activity by Altering Protein Dynamics with Solvent.
Authors: Duff Jr., M.R. / Borreguero, J.M. / Cuneo, M.J. / Ramanathan, A. / He, J. / Kamath, G. / Chennubhotla, S.C. / Meilleur, F. / Howell, E.E. / Herwig, K.W. / Myles, D.A.A. / Agarwal, P.K.
History
DepositionJan 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,16510
Polymers36,0412
Non-polymers1,1258
Water5,837324
1
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6687
Polymers18,0201
Non-polymers6486
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4973
Polymers18,0201
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.946, 91.946, 73.088
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Dihydrofolate reductase


Mass: 18020.326 Da / Num. of mol.: 2 / Mutation: N37D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: folA, A4X18_04670, A5958_06030, A6803_16755, A6804_06290, A6I92_00465, A8V37_23295, A9D65_12475, A9R57_20685, AA102_14635, AC067_04030, AC789_1c00510, ACU57_16280, ACU90_27155, AGA26_05675, ...Gene: folA, A4X18_04670, A5958_06030, A6803_16755, A6804_06290, A6I92_00465, A8V37_23295, A9D65_12475, A9R57_20685, AA102_14635, AC067_04030, AC789_1c00510, ACU57_16280, ACU90_27155, AGA26_05675, AKG99_14190, AM266_01265, AM270_12270, AMK83_01385, AML07_23835, AN206_21390, APT94_27185, APU18_01950, APZ14_15415, AUQ01_20785, AUS26_14425, AWF22_24845, AWG90_06875, AWH59_13130, AXE68_21355, BBZ52_00455, BHF46_08505, ECONIH1_00280, ECs0051, EL75_3711, EL79_3822, EL80_3768, GJ11_00260, GJ12_00260, HW42_03855, IY32_08385, JD73_13725, MJ49_06800, OK10_07960, OO96_05335, PU06_14795, PU21_08285, PU33_00085, SY51_00265, UC41_15235, UN86_27670, WM48_00255, WQ89_20085, WR15_01730
Production host: Escherichia coli (E. coli)
References: UniProt: C3TR70, UniProt: P0ABQ4*PLUS, dihydrofolate reductase

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M CaCl2, 20-35% PEG 6000, 0.1M NaHEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 32525 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 17.66 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.296 / Net I/σ(I): 13.2 / Num. measured all: 261190
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.8-1.868.10.5191.092199.5
1.86-1.947.20.4382.749199.7
1.94-2.038.20.3031.314199.8
2.03-2.138.40.1660.9281100
2.13-2.277.60.2021.97199.9
2.27-2.447.90.1341.336199.9
2.44-2.698.60.0910.9281100
2.69-3.088.50.0831.0411100
3.08-3.887.40.0620.927197.1
3.88-108.30.0510.949199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EAJ

5eaj


Resolution: 1.8→23.297 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2532 1613 5.07 %
Rwork0.2067 --
obs0.2091 31789 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.62 Å2 / Biso mean: 22.8323 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 1.8→23.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 73 324 2931
Biso mean--27.79 29.43 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032782
X-RAY DIFFRACTIONf_angle_d0.7143801
X-RAY DIFFRACTIONf_chiral_restr0.049394
X-RAY DIFFRACTIONf_plane_restr0.005503
X-RAY DIFFRACTIONf_dihedral_angle_d14.2241644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.85210.23621370.235252799
1.8521-1.91190.50571210.3617228589
1.9119-1.98020.39461170.3542244595
1.9802-2.05940.24841420.2192577100
2.0594-2.15310.28321460.22072562100
2.1531-2.26650.37661250.2908243995
2.2665-2.40840.28131130.2291249296
2.4084-2.59410.25711570.20362541100
2.5941-2.85470.22611320.19932603100
2.8547-3.26690.23721320.19842594100
3.2669-4.11220.22241600.1605247196
4.1122-100.18311310.1493264099

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