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- PDB-4qle: Crystal structure of I14A DHFR mutant complexed with folate and NADP+ -

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Basic information

Entry
Database: PDB / ID: 4qle
TitleCrystal structure of I14A 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: 1.35 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
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3246
Polymers35,9552
Non-polymers2,3704
Water6,017334
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1623
Polymers17,9771
Non-polymers1,1852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1623
Polymers17,9771
Non-polymers1,1852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.115, 59.515, 74.227
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrofolate reductase


Mass: 17977.260 Da / Num. of mol.: 2 / Fragment: DIHYDROFOLATE REDUCTASE / Mutation: I14A
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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium acetate, 20% w/v PEG 3350, 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: 0.855 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 9, 2011
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.855 Å / Relative weight: 1
ReflectionResolution: 1.35→73.88 Å / Num. all: 66630 / Num. obs: 66630 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 21.22
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RX2

1rx2


Resolution: 1.35→30.48 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.479 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18134 3379 5.1 %RANDOM
Rwork0.13372 ---
obs0.13617 63228 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.511 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.62 Å2
2---0.52 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 143 334 3005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192844
X-RAY DIFFRACTIONr_bond_other_d0.0010.022555
X-RAY DIFFRACTIONr_angle_refined_deg2.1592.0013901
X-RAY DIFFRACTIONr_angle_other_deg1.19835895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70124.091132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13515439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0651519
X-RAY DIFFRACTIONr_chiral_restr0.130.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213227
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02664
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_it1.6771.51671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.73622721
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.46731192
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0234.51207
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.92435399
X-RAY DIFFRACTIONr_sphericity_free29.05588
X-RAY DIFFRACTIONr_sphericity_bonded19.26255563
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 262 -
Rwork0.205 4594 -
obs--99.92 %

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