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- PDB-4qlf: Crystal structure of I14G DHFR mutant complexed with folate and NADP+ -

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Basic information

Entry
Database: PDB / ID: 4qlf
TitleCrystal structure of I14G DHFR mutant complexed with folate and NADP+
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate-reductase like fold/Alpha and beta proteins (a/b) / oxidoreductase activity / NADP(H) binding
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsStojkovic, V. / Gakhar, L. / Kohen, A.
CitationJournal: J.Phys.Chem.B / Year: 2015
Title: Free energy simulations of active-site mutants of dihydrofolate reductase.
Authors: Doron, D. / Stojkovic, V. / Gakhar, L. / Vardi-Kilshtain, A. / Kohen, A. / Major, D.T.
History
DepositionJun 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1483
Polymers17,9631
Non-polymers1,1852
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.489, 34.431, 134.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 17963.234 Da / Num. of mol.: 1 / Fragment: DIHYDROFOLATE REDUCTASE / Mutation: I14G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, BN896_0046 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6N356, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.9 M LiCl, 36% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 8, 2010
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→67.12 Å / Num. all: 27985 / Num. obs: 27985 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.1
Reflection shellResolution: 1.44→1.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3 / % possible all: 76.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0071refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RX2

1rx2


Resolution: 1.44→33.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.236 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20626 1446 5.2 %RANDOM
Rwork0.18151 ---
obs0.18284 26481 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.44→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 63 155 1461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191343
X-RAY DIFFRACTIONr_bond_other_d0.0010.021208
X-RAY DIFFRACTIONr_angle_refined_deg2.41921834
X-RAY DIFFRACTIONr_angle_other_deg1.03132782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61324.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28615204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.399158
X-RAY DIFFRACTIONr_chiral_restr0.1590.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211503
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.341.628629
X-RAY DIFFRACTIONr_mcbond_other2.3031.626627
X-RAY DIFFRACTIONr_mcangle_it3.5052.416781
X-RAY DIFFRACTIONr_mcangle_other3.4772.415781
X-RAY DIFFRACTIONr_scbond_it3.6172.005714
X-RAY DIFFRACTIONr_scbond_other3.6272.008707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5022.8561054
X-RAY DIFFRACTIONr_long_range_B_refined7.94614.5911596
X-RAY DIFFRACTIONr_long_range_B_other7.94414.5921597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.441→1.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 56 -
Rwork0.26 1237 -
obs--61.6 %

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