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- PDB-45pc: 6-conformation model of Escherichia coli dihydrofolate reductase ... -

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Basic information

Entry
Database: PDB / ID: 45pc
Title6-conformation model of Escherichia coli dihydrofolate reductase at 100K
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / folate reductase / tetrahydrofolate regulation
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / 10-formyltetrahydrofolate biosynthetic process / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / one-carbon metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / 10-formyltetrahydrofolate biosynthetic process / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / one-carbon metabolic process / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / NADP binding / response to antibiotic / response to xenobiotic stimulus / 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 str. K-12 substr. MC4100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsPassmore, S.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT220100405 Australia
Citation
Journal: Biorxiv / Year: 2026
Title: Optimizing the connectivity of protein conformations to untangle ensemble refinement
Authors: Passmore, S.K. / Holton, J.M. / Zatsepin, N.A. / Martin, A.V.
#1: Journal: Structure / Year: 2014
Title: Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.
Authors: Keedy, D.A. / van den Bedem, H. / Sivak, D.A. / Petsko, G.A. / Ringe, D. / Wilson, M.A. / Fraser, J.S.
History
DepositionSep 5, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Remark 0THIS ENTRY 45PC REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4PSS, DETERMINED BY D.A. ...THIS ENTRY 45PC REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4PSS, DETERMINED BY D.A.Keedy, H.van den Bedem, D.A.Sivak, G.A.Petsko, D.Ringe, M.A.Wilson, J.S.Fraser.

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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)19,3816
Polymers18,0511
Non-polymers1,3305
Water47,9382661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-18 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.960, 44.823, 98.254
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

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Protein , 1 types, 1 molecules A

#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 str. K-12 substr. MC4100 (bacteria)
Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase

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Non-polymers , 5 types, 2666 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2661 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.62 % / Description: author used sf file from pdb entry 4PSS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17% PEG 400, 20 mM imidazole pH 7.0, 125 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.849→40.78 Å / Num. obs: 130200 / % possible obs: 98.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 7.68 Å2 / Rsym value: 0.049 / Net I/σ(I): 36.3
Reflection shellResolution: 0.85→0.88 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12585 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX2.0_5793refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.85→40.78 Å / SU ML: 0.0695 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 7.8622
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.0809 1998 1.54 %
Rwork0.0638 128084 -
obs0.0641 130082 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 7.47 Å2
Refinement stepCycle: LAST / Resolution: 0.85→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 83 2661 4014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01048320
X-RAY DIFFRACTIONf_angle_d1.335311384
X-RAY DIFFRACTIONf_chiral_restr0.09061188
X-RAY DIFFRACTIONf_plane_restr0.01191438
X-RAY DIFFRACTIONf_dihedral_angle_d16.69273305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.870.25521360.248704X-RAY DIFFRACTION94.63
0.87-0.890.23521420.18149061X-RAY DIFFRACTION97.91
0.89-0.920.1711410.13659067X-RAY DIFFRACTION98.33
0.92-0.950.12841410.10229063X-RAY DIFFRACTION98.18
0.95-0.980.11491410.08439062X-RAY DIFFRACTION98.19
0.98-1.020.09431430.07359094X-RAY DIFFRACTION97.97
1.02-1.070.08241410.05529021X-RAY DIFFRACTION97.36
1.07-1.130.05831410.04739032X-RAY DIFFRACTION97.15
1.13-1.20.06921410.04489029X-RAY DIFFRACTION96.94
1.2-1.290.06581420.04849105X-RAY DIFFRACTION97.86
1.29-1.420.06361440.05119251X-RAY DIFFRACTION98.73
1.42-1.620.06941460.05289325X-RAY DIFFRACTION99.28
1.62-2.050.07171480.069474X-RAY DIFFRACTION99.92
2.05-40.780.07551510.06079796X-RAY DIFFRACTION99.75

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