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- PDB-2gqv: High-resolution structure of a plasmid-encoded dihydrofolate redu... -

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Basic information

Entry
Database: PDB / ID: 2gqv
TitleHigh-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site
ComponentsDihydrofolate reductase type 2
KeywordsOXIDOREDUCTASE / anisotropic refinement / atomic-resolution structure / folate metabolism / plasmid-encoded R67 DHFR / TMP-resistant DHFR
Function / homology
Function and homology information


response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / response to xenobiotic stimulus / response to antibiotic
Similarity search - Function
Dihydrofolate reductase, type II / R67 dihydrofolate reductase / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, beta-domain superfamily / Electron transport accessory-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Dihydrofolate reductase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsNarayana, N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D(2)-symmetric active site.
Authors: Narayana, N.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site.
Authors: Narayana, N. / Matthews, D.A. / Howell, E.E. / Nguyen-huu, X.
#2: Journal: Biochemistry / Year: 1986
Title: Crystal structure of a novel trimethoprim-resistant dihydrofolate reductase specified in Escherichia coli by R-plasmid R67.
Authors: Matthews, D.A. / Smith, S.L. / Baccanari, D.P. / Burchall, J.J. / Oatley, S.J. / Kraut, J.
History
DepositionApr 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase type 2


Theoretical massNumber of molelcules
Total (without water)6,7331
Polymers6,7331
Non-polymers00
Water3,441191
1
A: Dihydrofolate reductase type 2

A: Dihydrofolate reductase type 2

A: Dihydrofolate reductase type 2

A: Dihydrofolate reductase type 2


Theoretical massNumber of molelcules
Total (without water)26,9304
Polymers26,9304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Unit cell
Length a, b, c (Å)68.050, 68.050, 52.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-67-

GLN

21A-234-

HOH

31A-243-

HOH

DetailsThe biological assembly is comprised of four subunits generated by symmetry axes. The crystallographic 222 symmetry generates the biologically active tetramer. x,y,z; -x+1,-y+1,z; y,x,-z+1; -y+1,-x+1,-z+1

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Components

#1: Protein Dihydrofolate reductase type 2 / Dihydrofolate reductase type II


Mass: 6732.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Strain: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING PLASMID PLZ1
Production host: Escherichia coli (E. coli) / References: UniProt: P00383, dihydrofolate reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-Hcl buffer, 25% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9495 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9495 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. all: 22453 / Num. obs: 19914 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 8.5 % / Biso Wilson estimate: 9.7 Å2 / Rsym value: 0.042 / Net I/σ(I): 21.4
Reflection shellResolution: 1.1→1.14 Å / Rsym value: 0.34 / % possible all: 58

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VIE

1vie


Resolution: 1.1→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.153 1121 -RANDOM
Rwork0.099 ---
obs0.105 19914 86 %-
all-22389 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms455 0 0 191 646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_from_restr_planes0.0284
X-RAY DIFFRACTIONs_zero_chiral_vol0.118
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.175
X-RAY DIFFRACTIONs_similar_dist0.034
X-RAY DIFFRACTIONs_approx_iso_adps0.103
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.012
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.034
LS refinement shellHighest resolution: 1.1 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.153 1121 -
Rwork0.105 --
obs-22389 89 %

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