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- PDB-5eaj: Crystal structure of DHFR in 0% Isopropanol -

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Basic information

Entry
Database: PDB / ID: 5eaj
TitleCrystal structure of DHFR in 0% Isopropanol
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dynamics
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / NADP+ 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 / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 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
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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 / 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)37,1059
Polymers36,0412
Non-polymers1,0657
Water4,864270
1
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6086
Polymers18,0201
Non-polymers5885
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)91.947, 91.947, 73.097
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#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
#2: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 270 / 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: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M CaCl2, 20-35 % (w/v) PEG 6000, 0.1M NaHEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 38279 / Num. obs: 38279 / % possible obs: 99.1 % / Redundancy: 8.4 % / Biso Wilson estimate: 22.79 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.357 / Net I/av σ(I): 38.455 / Net I/σ(I): 15.8 / Num. measured all: 320420
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.764.50.52536331.02394.6
1.76-1.836.90.41837701.00598.4
1.83-1.918.40.31538211.09299.2
1.91-2.028.90.22938331.227100
2.02-2.149.10.16638461.444100
2.14-2.319.30.11438591.542100
2.31-2.549.30.08338531.433100
2.54-2.919.20.06738541.81100
2.91-3.669.10.04738981.5100
3.66-408.80.03739121.15399.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.6.2_432)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RD7

1rd7


Resolution: 1.701→38.916 Å / FOM work R set: 0.8315 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1911 5 %
Rwork0.1978 36334 -
obs0.1992 38245 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.42 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 104.52 Å2 / Biso mean: 30.72 Å2 / Biso min: 9.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.8982 Å20 Å20 Å2
2---1.8982 Å20 Å2
3---3.7964 Å2
Refinement stepCycle: final / Resolution: 1.701→38.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 69 270 2873
Biso mean--32.25 35.7 -
Num. residues----317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042835
X-RAY DIFFRACTIONf_angle_d0.8583884
X-RAY DIFFRACTIONf_chiral_restr0.059404
X-RAY DIFFRACTIONf_plane_restr0.003517
X-RAY DIFFRACTIONf_dihedral_angle_d12.9671054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7012-1.74380.35311140.2912417253193
1.7438-1.79090.2881410.25882525266698
1.7909-1.84360.30931290.24862594272399
1.8436-1.90310.29451520.22882571272399
1.9031-1.97110.24841180.227326122730100
1.9711-2.05010.27941330.228226192752100
2.0501-2.14340.25151390.215926132752100
2.1434-2.25640.22031290.212226212750100
2.2564-2.39770.25781400.203326252765100
2.3977-2.58280.25151430.204825892732100
2.5828-2.84260.28061220.212126482770100
2.8426-3.25380.24851440.206826382782100
3.2538-4.09870.18311490.170926192768100
4.0987-38.92660.17161580.16322643280199

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