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- PDB-7lvc: E. coli DHFR by Native Mn,P,S-SAD at Room Temperature -

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Basic information

Entry
Database: PDB / ID: 7lvc
TitleE. coli DHFR by Native Mn,P,S-SAD at Room Temperature
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Dihydrofolate Reductase
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 / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
FOLIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsGreisman, J.B. / Dalton, K.M. / Hekstra, D.R.
Funding support United States, 3items
OrganizationGrant numberCountry
Searle Scholars ProgramSSP-2018-3240 United States
George W. Merck Fund in the New York Community Trust338034 United States
National Science Foundation (NSF, United States)DGE1745303 United States
Citation
#1: Journal: Acta Crystallogr.,Sect.D
Title: Native SAD phasing at room temperature
Authors: Greisman, J.B. / Dalton, K.M. / Sheehan, C.J. / Klureza, M.A. / Kurinov, I. / Hekstra, D.R.
History
DepositionFeb 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 17, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5118
Polymers18,0511
Non-polymers1,4597
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-12 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.297, 45.552, 99.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Dihydrofolate reductase


Mass: 18051.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 mM imadazole (pH 5.4-5.8), 16-21% PEG 400, 125 mM MnCl2
PH range: 5.4 - 5.8

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Data collection

DiffractionMean temperature: 295 K / Ambient temp details: ambient / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.892 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.892 Å / Relative weight: 1
ReflectionResolution: 1.7→49.52 Å / Num. obs: 27966 / % possible obs: 85.52 % / Redundancy: 29.4 % / Biso Wilson estimate: 12.78 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1012 / Rpim(I) all: 0.01671 / Rrim(I) all: 0.1026 / Net I/σ(I): 30.18
Reflection shellResolution: 1.7→1.77 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.2227 / Mean I/σ(I) obs: 4.42 / Num. unique obs: 720 / CC1/2: 0.945 / CC star: 0.986 / Rpim(I) all: 0.1143 / Rrim(I) all: 0.2512 / % possible all: 22.11

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Processing

Software
NameVersionClassification
DIALS3.1.4data reduction
Aimless0.7.4data scaling
AutoSol1.18.2_3874phasing
PHENIX1.18.2_3874model building
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→49.52 Å / SU ML: 0.1196 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.4225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1719 1376 4.92 %
Rwork0.139 26590 -
obs0.1407 27966 85.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 85 106 1461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521530
X-RAY DIFFRACTIONf_angle_d0.93342109
X-RAY DIFFRACTIONf_chiral_restr0.056214
X-RAY DIFFRACTIONf_plane_restr0.0049277
X-RAY DIFFRACTIONf_dihedral_angle_d16.0591560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.1663280.1656692X-RAY DIFFRACTION22.11
1.77-1.840.1877970.142110X-RAY DIFFRACTION67.55
1.84-1.920.17141290.13472597X-RAY DIFFRACTION83.36
1.92-2.020.18351180.12492904X-RAY DIFFRACTION91.88
2.02-2.150.19511750.13522949X-RAY DIFFRACTION95.59
2.15-2.310.18421660.12813035X-RAY DIFFRACTION97.95
2.31-2.550.16271430.14383060X-RAY DIFFRACTION98.71
2.55-2.910.18291460.13733104X-RAY DIFFRACTION98.87
2.92-3.670.17582040.14413049X-RAY DIFFRACTION99.6
3.67-49.520.14911700.14393090X-RAY DIFFRACTION99.33
Refinement TLS params.Method: refined / Origin x: 23.575962697 Å / Origin y: 21.4047757535 Å / Origin z: 35.5768107525 Å
111213212223313233
T0.0326715003552 Å2-0.000117353696921 Å2-0.00823188052927 Å2-0.0454758860491 Å2-0.00807141520864 Å2--0.0395182220841 Å2
L0.817551282812 °20.216153636002 °2-0.0882851025547 °2-0.814519152635 °2-0.0811836610434 °2--0.777899409626 °2
S0.00130150490191 Å °0.0654853416154 Å °-0.00982396989333 Å °-0.00389785319831 Å °0.027223160895 Å °0.0785503286464 Å °0.00647845942123 Å °-0.0419747501988 Å °0.084187897695 Å °
Refinement TLS groupSelection details: all

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