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- PDB-2w9t: Staphylococcus aureus S1:DHFR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2w9t
TitleStaphylococcus aureus S1:DHFR
ComponentsDIHYDROFOLATE REDUCTASE TYPE 1
KeywordsOXIDOREDUCTASE / ANTIBIOTIC RESISTANCE / STAPHYLOCOCCUS AUREUS / DHFR / NADP / PLASMID / TRIMETHOPRIM / TRIMETHOPRIM RESISTANCE / ONE-CARBON METABOLISM / METHOTREXATE RESISTANCE
Function / homology
Function and homology information


response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydrofolate reductase type 1 from Tn4003
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSoutter, H.H. / Miller, J.R.
CitationJournal: Proteins / Year: 2009
Title: Structural Comparison of Chromosomal and Exogenous Dihydrofolate Reductase from Staphylococcus Aureus in Complex with the Potent Inhibitor Trimethoprim.
Authors: Heaslet, H. / Harris, M. / Fahnoe, K. / Sarver, R. / Putz, H. / Chang, J. / Subramanyam, C. / Barreiro, G. / Miller, J.R.
History
DepositionJan 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE TYPE 1
B: DIHYDROFOLATE REDUCTASE TYPE 1


Theoretical massNumber of molelcules
Total (without water)37,0022
Polymers37,0022
Non-polymers00
Water2,450136
1
A: DIHYDROFOLATE REDUCTASE TYPE 1


Theoretical massNumber of molelcules
Total (without water)18,5011
Polymers18,5011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DIHYDROFOLATE REDUCTASE TYPE 1


Theoretical massNumber of molelcules
Total (without water)18,5011
Polymers18,5011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.090, 71.637, 54.132
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DIHYDROFOLATE REDUCTASE TYPE 1 / DEHYDROFOLATE REDUCTASE


Mass: 18500.988 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: EXOGENOUS DRUG-RESISTANT VARIANT / Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13955, dihydrofolate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 49 TO GLU ENGINEERED RESIDUE IN CHAIN A, ASN 131 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, ASN 49 TO GLU ENGINEERED RESIDUE IN CHAIN A, ASN 131 TO ASP ENGINEERED RESIDUE IN CHAIN B, ASN 49 TO GLU ENGINEERED RESIDUE IN CHAIN B, ASN 131 TO ASP

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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: 2.73 Å3/Da / Density % sol: 54.59 % / Description: NONE
Crystal growpH: 7 / Details: 2.1 M MALIC ACID PH 7.0

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 20, 2007 / Details: SI
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 17017 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→71.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.206 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 861 5.1 %RANDOM
Rwork0.175 ---
obs0.179 16136 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.11 Å2
2---1.23 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.35→71.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 0 136 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222674
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.41.9363634
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1735324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81824.638138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77515458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7361514
X-RAY DIFFRACTIONr_chiral_restr0.2060.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022060
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.21079
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21758
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2141
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3540.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8331.51669
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.06522623
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.52231148
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.6654.51011
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 40 -
Rwork0.261 840 -
obs--70.23 %

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