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- PDB-4klx: Crystal structure of dihydrofolate reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 4klx
TitleCrystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation.
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 / Chem-ETE / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.23 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)40,8875
Polymers39,6652
Non-polymers1,2233
Water9,422523
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5483
Polymers19,8321
Non-polymers7152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3402
Polymers19,8321
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.410, 63.060, 78.160
Angle α, β, γ (deg.)90.000, 100.820, 90.000
Int Tables number4
Space group name H-MP1211

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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) / Gene: dfrA, folA, H37Rv, 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-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 1.98 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 4, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.23→76.77 Å / Num. all: 88928 / Num. obs: 88928 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rsym value: 0.107 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.23-1.33.20.4741.641584128000.47497.9
1.3-1.383.40.4031.941414122880.40399.9
1.38-1.473.30.3112.538769116080.31199.9
1.47-1.593.30.2243.435544107380.22499.8
1.59-1.743.30.1554.93243199110.15599.5
1.74-1.943.20.1066.72873189170.10699.2
1.94-2.253.10.0778.72474178830.07799
2.25-2.753.10.0699.32081366730.06999.1
2.75-3.893.30.0589.91713252240.05899.9
3.89-19.873.20.0579.5931828860.05798.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.87 Å
Translation2.5 Å19.87 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.23→19.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2395 / WRfactor Rwork: 0.1788 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8676 / SU B: 2.029 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0533 / SU Rfree: 0.0589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 4452 5 %RANDOM
Rwork0.1804 ---
obs0.1835 88844 99.14 %-
all-88928 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.36 Å2 / Biso mean: 12.3997 Å2 / Biso min: 2.78 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.23→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 76 523 3096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192671
X-RAY DIFFRACTIONr_angle_refined_deg2.481.9833652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1255331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52121.282117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28815406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.61534
X-RAY DIFFRACTIONr_chiral_restr0.2730.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212046
X-RAY DIFFRACTIONr_rigid_bond_restr6.99232671
X-RAY DIFFRACTIONr_sphericity_free33.0845139
X-RAY DIFFRACTIONr_sphericity_bonded11.27952984
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 291 -
Rwork0.247 5921 -
all-6212 -
obs--95.79 %

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