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- PDB-5z6f: High-pressure Crystal Structure Analysis of DHFR(0.1 MPa) -

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Basic information

Entry
Database: PDB / ID: 5z6f
TitleHigh-pressure Crystal Structure Analysis of DHFR(0.1 MPa)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / M20 loop closed form
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, 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsWatanabe, N. / Nagae, T. / Yamada, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS KAKENHI21657027 Japan
JSPS KAKENHI24657071 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP.
Authors: Nagae, T. / Yamada, H. / Watanabe, N.
History
DepositionJan 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,5633
Polymers18,3781
Non-polymers1,1852
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-1 kcal/mol
Surface area7980 Å2
Unit cell
Length a, b, c (Å)34.114, 45.913, 99.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrofolate reductase


Mass: 18377.736 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 400, CaCl, imidazole buffer

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.75 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.8→41.66 Å / Num. obs: 15050 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.717

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RX2

1rx2


Resolution: 1.801→41.658 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.28
RfactorNum. reflection% reflection
Rfree0.2101 757 5.05 %
Rwork0.1774 --
obs0.1791 15003 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→41.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 80 87 1449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071403
X-RAY DIFFRACTIONf_angle_d1.1751918
X-RAY DIFFRACTIONf_dihedral_angle_d9.203800
X-RAY DIFFRACTIONf_chiral_restr0.064199
X-RAY DIFFRACTIONf_plane_restr0.006245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8014-1.94050.22711620.20042755X-RAY DIFFRACTION100
1.9405-2.13570.20231380.17962816X-RAY DIFFRACTION100
2.1357-2.44470.22631380.1712836X-RAY DIFFRACTION100
2.4447-3.080.21161610.18112850X-RAY DIFFRACTION100
3.08-41.66870.20291580.17312989X-RAY DIFFRACTION100

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