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- PDB-5e8q: Crystal structure of DHFR in 20% Isopropanol -

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Basic information

Entry
Database: PDB / ID: 5e8q
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 / Resolution: 1.8 Å
AuthorsCuneo, M.J. / Agarwal, P.K.
CitationJournal: To Be Published
Title: Solvent conditions control enzyme dynamics and catalysis
Authors: Borrguero, J.M. / Cuneo, M.J. / Agarwal, P.K.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: folA, AA953_06220, ABE89_23390, ABE90_01590, ABE91_11465, ABE92_27580, ABE93_03540, ABE94_26505, ABE95_19105, AC789_1c00510, ACM16_01115, ACM17_00910, ACM18_00225, ACM19_01115, ACM20_00925, ...Gene: folA, AA953_06220, ABE89_23390, ABE90_01590, ABE91_11465, ABE92_27580, ABE93_03540, ABE94_26505, ABE95_19105, AC789_1c00510, ACM16_01115, ACM17_00910, ACM18_00225, ACM19_01115, ACM20_00925, ACM21_22820, BN1008_2275, ECONIH1_00280, ECs0051, EL75_3711, EL79_3822, EL80_3768, HW43_03985, IY32_08385, JD73_13725, NMECO18_25965, PD07_16380, PU06_14795, PU15_01135, PU21_08285, PU33_00085, PU38_11910, PU53_21230, PU69_06270, PU71_09850, PU73_17465, RR31_00265, SK64_04362, SK65_04102, SK81_04106, SY51_00265, TZ57_00270, UC21_17710, UC41_15235, UN86_27670, UN92_06125, WQ64_08430, WQ65_17175, WQ66_04025, WQ69_03315, WQ70_09735, WQ71_08985, WQ72_04470, WQ73_14425, WQ74_13220, WQ77_00770, WQ79_09130, WQ84_04435, WQ86_16125, WQ88_00770, WQ91_15025, WQ92_19155, WQ95_08145, WQ99_15285, WR00_12370, WR01_07485, WR03_05655, WR04_00040, WR05_03890, WR12_01840, WR13_10745, WR16_15930, WR17_04125, WR18_06540, WR19_18465, WR23_10335, WR24_10640, XB00_01295, XB01_19915
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL
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
#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, 2012
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. all: 32525 / Num. obs: 32525 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 17.63 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.296 / Net I/av σ(I): 19.524 / Net I/σ(I): 13.2 / Num. measured all: 261190
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.868.10.5195.432291.09299.5
1.86-1.947.20.43832322.74999.7
1.94-2.038.20.30332481.31499.8
2.03-2.138.40.16632760.928100
2.13-2.277.60.20232371.9799.9
2.27-2.447.90.13432701.33699.9
2.44-2.698.60.09132420.928100
2.69-3.088.50.08332871.041100
3.08-3.887.40.06231800.92797.1
3.88-408.30.05133240.94999.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DRC

3drc


Resolution: 1.8→23.297 Å / FOM work R set: 0.8097 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1613 5.07 %Random
Rwork0.1973 30176 --
obs0.2002 31789 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.845 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 112.37 Å2 / Biso mean: 26.33 Å2 / Biso min: 6.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.3907 Å20 Å20 Å2
2---0.3907 Å2-0 Å2
3---0.7815 Å2
Refinement stepCycle: final / Resolution: 1.8→23.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 73 324 2931
Biso mean--33.04 33.09 -
Num. residues----317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122782
X-RAY DIFFRACTIONf_angle_d1.3753801
X-RAY DIFFRACTIONf_chiral_restr0.094394
X-RAY DIFFRACTIONf_plane_restr0.007503
X-RAY DIFFRACTIONf_dihedral_angle_d14.5791028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7992-1.85210.23741370.20072527266499
1.8521-1.91190.46181210.31892285240689
1.9119-1.98020.41791170.35242445256295
1.9802-2.05940.26371420.21225772719100
2.0594-2.15310.26751460.205425622708100
2.1531-2.26650.37341250.28222439256495
2.2665-2.40840.28011130.22582492260596
2.4084-2.59410.25571570.188825412698100
2.5941-2.85470.24511320.191326032735100
2.8547-3.26690.22771320.187725942726100
3.2669-4.11220.22311600.15512471263196
4.1122-23.29860.18341310.14422640277199

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