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- PDB-4fhb: Enhancing DHFR catalysis by binding of an allosteric regulator na... -

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Basic information

Entry
Database: PDB / ID: 4fhb
TitleEnhancing DHFR catalysis by binding of an allosteric regulator nanobody (Nb179)
Components
  • Dihydrofolate reductase
  • Nb179
KeywordsOxidoreductase/protein binding / Nanobody / Dihydrofolate reductase / Allosteric activator / Reductase / Oxidoreductase-protein binding complex
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOyen, D.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Mechanistic analysis of allosteric and non-allosteric effects arising from nanobody binding to two epitopes of the dihyrofolate reductase of Escherichia coli.
Authors: Oyen, D. / Wechselberger, R. / Srinivasan, V. / Steyaert, J. / Barlow, J.N.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
D: Nb179
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0844
Polymers32,9002
Non-polymers1,1852
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.889, 72.889, 254.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dihydrofolate reductase /


Mass: 18019.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Antibody Nb179


Mass: 14880.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium chloride, 0.1M Na HEPES, 25% w/v PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: PILATUS 2M-F / Detector: PIXEL / Date: Mar 28, 2012
RadiationMonochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.8→44 Å / Num. all: 262820 / Num. obs: 10672 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.95 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→42.379 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.296 506 4.77 %RANDOM
Rwork0.2174 ---
all0.2212 10599 --
obs0.2212 10599 99.97 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.591 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8152 Å20 Å20 Å2
2---1.8152 Å2-0 Å2
3---3.6304 Å2
Refinement stepCycle: LAST / Resolution: 2.8→42.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 80 0 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082334
X-RAY DIFFRACTIONf_angle_d1.1743183
X-RAY DIFFRACTIONf_dihedral_angle_d16.458818
X-RAY DIFFRACTIONf_chiral_restr0.069331
X-RAY DIFFRACTIONf_plane_restr0.006409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.08180.33571210.24652422X-RAY DIFFRACTION100
3.0818-3.52760.35421260.21942461X-RAY DIFFRACTION100
3.5276-4.44360.27511230.19822505X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0479-0.61020.8865.3433-1.22531.725-0.06940.55780.0568-0.62770.02520.5229-0.12710.1831-0.10310.3666-0.11180.06360.3426-0.05680.272425.8863-13.197319.5116
26.8251-2.53961.49062.97171.14181.74540.3517-0.18820.0920.3427-0.22530.96680.0433-0.3722-0.18820.2975-0.04680.08160.35750.24040.776316.6695-19.6226.2122
33.78460.7925-0.44854.75351.01731.581-0.07310.3898-0.9792-0.86440.24690.99460.0104-0.13250.09190.3958-0.0457-0.2310.2686-0.00080.852512.5431-18.00869.9691
41.88580.0183-1.82821.66060.61836.28250.00770.3052-0.2662-0.38190.12321.5068-0.6893-1.138-0.34440.35120.0762-0.1220.21330.12380.83767.2947-9.779112.6454
54.8148-0.95720.07362.9638-0.55022.5068-0.24210.39681.0023-0.00820.47930.3678-0.70720.2392-0.08160.7594-0.13970.05310.26440.02910.503722.4023-5.948120.2888
61.4911-0.9792-0.20542.33781.05832.60470.0099-0.30730.3007-0.01860.24340.4867-0.87290.1553-0.13990.3903-0.0350.23310.31920.00460.397824.0688-12.107532.314
78.7749-4.18390.02114.6258-0.87837.0780.08940.07610.60750.1948-0.1449-0.0942-0.6601-0.2689-1.48430.7597-0.04010.40740.2690.02750.490718.583-6.339530.5291
84.3640.12820.62672.21510.96981.08520.0789-1.0515-0.16190.04130.0398-0.02690.4619-0.13830.03690.30540.0452-0.03020.4349-0.25280.337841.93130.347443.3629
92.37690.10120.18172.20220.52511.5266-0.3976-0.18720.5258-0.35840.5671-0.5184-0.33980.5984-0.0120.4922-0.06730.14890.2453-0.32150.318346.5317-2.586833.0343
101.10940.52431.74133.92331.32472.80150.0738-0.44320.1218-0.21910.355-0.8111-0.00440.2852-0.34270.50630.0157-0.04790.4642-0.27530.33447.6057-4.472741.6411
116.21634.47443.95014.38572.65193.7444-0.0054-0.28720.7022-0.00040.1304-0.1875-0.02040.07940.17550.5424-0.0530.02670.2534-0.13290.397239.08990.239430.6528
124.98820.72615.61013.409-0.65687.9222-0.26640.12170.3357-0.83090.53380.1512-0.1490.0231-0.15530.5687-0.0766-0.0410.4343-0.2010.473946.31015.840537.3542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:24)
2X-RAY DIFFRACTION2chain 'A' and (resseq 25:35)
3X-RAY DIFFRACTION3chain 'A' and (resseq 36:72)
4X-RAY DIFFRACTION4chain 'A' and (resseq 73:96)
5X-RAY DIFFRACTION5chain 'A' and (resseq 97:129)
6X-RAY DIFFRACTION6chain 'A' and (resseq 130:150)
7X-RAY DIFFRACTION7chain 'A' and (resseq 151:159)
8X-RAY DIFFRACTION8chain 'D' and (resseq 3:33)
9X-RAY DIFFRACTION9chain 'D' and (resseq 34:67)
10X-RAY DIFFRACTION10chain 'D' and (resseq 68:91)
11X-RAY DIFFRACTION11chain 'D' and (resseq 92:112)
12X-RAY DIFFRACTION12chain 'D' and (resseq 113:129)

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