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- PDB-5tvy: Computationally Designed Fentanyl Binder - Fen49 -

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Basic information

Entry
Database: PDB / ID: 5tvy
TitleComputationally Designed Fentanyl Binder - Fen49
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / Computational Design / Fentanyl
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsBick, M.J. / Greisen, P.J. / Morey, K.J. / Antunes, M.S. / La, D. / Sankaran, B. / Reymond, L. / Johnsson, K. / Medford, J.I. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5F32CA171572-03 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-13-1-0054 United States
Life Sciences Discovery Fund9598385 United States
CitationJournal: Elife / Year: 2017
Title: Computational design of environmental sensors for the potent opioid fentanyl.
Authors: Bick, M.J. / Greisen, P.J. / Morey, K.J. / Antunes, M.S. / La, D. / Sankaran, B. / Reymond, L. / Johnsson, K. / Medford, J.I. / Baker, D.
History
DepositionNov 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase A
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9684
Polymers41,0512
Non-polymers9172
Water11,241624
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9842
Polymers20,5251
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9842
Polymers20,5251
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.380, 79.568, 54.459
Angle α, β, γ (deg.)90.000, 101.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endo-1,4-beta-xylanase A / Xylanase A / 1 / 4-beta-D-xylan xylanohydrolase A


Mass: 20525.346 Da / Num. of mol.: 2 / Fragment: UNP residues 30-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: xynA, BSU18840 / Production host: Escherichia coli (E. coli) / References: UniProt: P18429, endo-1,4-beta-xylanase
#2: Chemical ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL / Polyethylene glycol


Mass: 458.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 1ul of protein at 20mg/ml mixed with 1ul of mother liquor, plus 0.2ul of a seed stock made from a previous crystallization drop. Crystallization condition is 0.1M Citric Acid pH 3.5, 25% PEG 3350.
Temp details: Temperature Controlled Crystal Incubator

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Liquid Nitrogen Cryo Stream
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.75141 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2016
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75141 Å / Relative weight: 1
ReflectionResolution: 1→44.333 Å / Num. obs: 181340 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 8.14 Å2 / Rmerge(I) obs: 0.058 / Net I/av σ(I): 21 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1-1.023.70.9730.890.557199.9
1.02-1.044.10.7931.220.6811100
1.04-1.064.40.6821.530.7541100
1.06-1.084.50.52820.8391100
1.08-1.14.50.4252.630.8821100
1.1-1.134.50.3373.440.9291100
1.13-1.154.50.2844.060.9481100
1.15-1.194.50.2534.80.9551100
1.19-1.224.50.2275.20.9611100
1.22-1.264.50.2026.290.9681100
1.26-1.34.60.186.710.9761100
1.3-1.364.60.1548.150.9811100
1.36-1.424.60.1299.690.9861100
1.42-1.494.60.10612.30.991100
1.49-1.594.60.08916.460.9931100
1.59-1.714.60.07820.070.9931100
1.71-1.884.60.06426.350.9951100
1.88-2.154.50.04536.770.9971100
2.15-2.714.60.03441.580.9981100
2.71-504.70.02354.120.9991100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.04 Å19.29 Å
Translation1.04 Å19.29 Å

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Processing

Software
NameVersionClassification
HKL-2000v708cdata reduction
HKL-2000v708cdata scaling
PHASER2.7.0phasing
Coot0.8.2model building
PHENIXdev_2841refinement
PDB_EXTRACT3.2data extraction
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fen49 Computational Design, with residues 63, 85-95 and 116-122 removed

Resolution: 1→44.333 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.88
Details: Interative rounds of model building in Coot and refinement in Phenix. Refinement in real and reciprocal space, all-atom (except H) anisotropic ADP refinement, occupancy refinement. ...Details: Interative rounds of model building in Coot and refinement in Phenix. Refinement in real and reciprocal space, all-atom (except H) anisotropic ADP refinement, occupancy refinement. Optimization of X-ray to stereochemistry and X-ray to ADP weights. Automatic addition of hydrogens to the model, and automatic correction of N/Q/H errors. Several rounds of updating waters during refinement. Manual inspection and correction of waters before the final round of refinement.
RfactorNum. reflection% reflection
Rfree0.1215 2254 1.24 %
Rwork0.108 --
obs0.1082 181281 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.62 Å2 / Biso mean: 13.2158 Å2 / Biso min: 4.91 Å2
Refinement stepCycle: final / Resolution: 1→44.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 132 648 3668
Biso mean--31.37 27.93 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073352
X-RAY DIFFRACTIONf_angle_d1.0584635
X-RAY DIFFRACTIONf_chiral_restr0.087469
X-RAY DIFFRACTIONf_plane_restr0.008603
X-RAY DIFFRACTIONf_dihedral_angle_d17.91118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9999-1.02160.251400.2604111151125599
1.0216-1.04540.23471400.20881113911279100
1.0454-1.07160.1751400.17341117511315100
1.0716-1.10050.15331400.14781113311273100
1.1005-1.13290.15631420.12641120211344100
1.1329-1.16950.11761390.10781113711276100
1.1695-1.21130.11271400.11118011320100
1.2113-1.25980.12021410.09691120411345100
1.2598-1.31710.13031410.09331115611297100
1.3171-1.38660.1081400.08861117711317100
1.3866-1.47350.10541420.08261119911341100
1.4735-1.58720.10361410.08011116511306100
1.5872-1.7470.09781410.08361126011401100
1.747-1.99980.09431410.08751120011341100
1.9998-2.51950.10981420.10041124611388100
2.5195-44.37690.12751440.11781133911483100

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