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- PDB-4km2: Crystal structure of Dihydrofolate reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 4km2
TitleCrystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation in complex with trimethoprim
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / reductase
Function / homology
Function and homology information


glycine biosynthetic process / NADP+ binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
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
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / TRIMETHOPRIM / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDias, M.V.B. / Tyrakis, P. / Blundell, T.L.
CitationJournal: Structure / Year: 2014
Title: Mycobacterium tuberculosis Dihydrofolate Reductase Reveals Two Conformational States and a Possible Low Affinity Mechanism to Antifolate Drugs.
Authors: Dias, M.V. / Tyrakis, P. / Domingues, R.R. / Paes Leme, A.F. / Blundell, T.L.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2606
Polymers39,6652
Non-polymers1,5954
Water10,971609
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6303
Polymers19,8321
Non-polymers7972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6303
Polymers19,8321
Non-polymers7972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.160, 65.280, 79.750
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: 19832.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dfrA, folA, MT2833, MTV002.28c, Rv2763c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)
References: UniProt: P0A546, UniProt: P9WNX1*PLUS, dihydrofolate reductase
#2: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N4O3 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M KCl, 0.01M MgCl2, 15% PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 8, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50.515 Å / Num. all: 65906 / Num. obs: 65906 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rsym value: 0.104 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.488.80.77118265593850.77198
1.48-1.578.90.5311.47970489520.53198.3
1.57-1.6790.3642.17592284340.36498.8
1.67-1.8190.25337152479150.25399
1.81-1.9890.1593.96612973140.15999.4
1.98-2.2190.1066.46022866640.10699.5
2.21-2.5690.094.15351859250.0999.8
2.56-3.1390.0619.44541150540.06199.9
3.13-4.438.90.04512.93530339780.045100
4.43-21.9928.40.037151916022850.03799.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→20.99 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.292 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 3336 5.1 %RANDOM
Rwork0.1406 ---
obs0.1437 65797 98.79 %-
all-65906 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.69 Å2 / Biso mean: 16.479 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 104 609 3201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192709
X-RAY DIFFRACTIONr_angle_refined_deg2.4322.0013710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44521.282117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95715419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6561534
X-RAY DIFFRACTIONr_chiral_restr0.1840.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212080
X-RAY DIFFRACTIONr_rigid_bond_restr6.89932709
X-RAY DIFFRACTIONr_sphericity_free35.0045146
X-RAY DIFFRACTIONr_sphericity_bonded13.70953100
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 220 -
Rwork0.233 4251 -
all-4471 -
obs--97.58 %

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