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- PDB-5tzo: Computationally Designed Fentanyl Binder - Fen49*-Complex -

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Basic information

Entry
Database: PDB / ID: 5tzo
TitleComputationally Designed Fentanyl Binder - Fen49*-Complex
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
Chem-7V7 / : / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 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 22, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
C: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,54215
Polymers61,3003
Non-polymers2,24212
Water12,863714
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2206
Polymers20,4331
Non-polymers7875
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)21,1815
Polymers20,4331
Non-polymers7474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1424
Polymers20,4331
Non-polymers7083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.070, 73.250, 136.640
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 Endo-1,4-beta-xylanase A / Xylanase A / 1 / 4-beta-D-xylan xylanohydrolase A


Mass: 20433.248 Da / Num. of mol.: 3 / 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-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide / Fentanyl


Mass: 336.471 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H28N2O
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Description: Rod-like crystals with longest dimension of approximately 200 microns.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M sodium phosphate, 0.8M potassium phosphate, 0.1M HEPES pH 7.5
Temp details: Temperature Stabilized 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: 0.999878 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2015
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999878 Å / Relative weight: 1
ReflectionResolution: 1.67→51.87 Å / Num. obs: 65282 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 13.02 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.2
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.69 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.5.6.phasing
Coot0.8model building
PHENIXdev_2463refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.67→51.87 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7
Details: Iterative rounds of model building in Coot and refinement in Phenix. Refinement parameters included real and reciprocal space, individual ADPs, Occupanices, Optimization of X-ray to ...Details: Iterative rounds of model building in Coot and refinement in Phenix. Refinement parameters included real and reciprocal space, individual ADPs, Occupanices, Optimization of X-ray to stereochemical and X-ray to ADP weights. Hydrogens were added automatically and Automatic correction of N/Q/H errors was used. Updated solvent model was used in the penultimate round of refinement. Manual modeling of solvent was conducted before the final round of refinement.
RfactorNum. reflection% reflection
Rfree0.2025 3322 5.1 %
Rwork0.1662 --
obs0.1681 65179 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.43 Å2
Refinement stepCycle: LAST / Resolution: 1.67→51.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 143 714 5115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064737
X-RAY DIFFRACTIONf_angle_d0.8426532
X-RAY DIFFRACTIONf_dihedral_angle_d16.052564
X-RAY DIFFRACTIONf_chiral_restr0.116664
X-RAY DIFFRACTIONf_plane_restr0.005834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.69390.31351360.262575X-RAY DIFFRACTION100
1.6939-1.71920.30631470.24942559X-RAY DIFFRACTION100
1.7192-1.7460.27611410.23432595X-RAY DIFFRACTION100
1.746-1.77470.2461260.21732574X-RAY DIFFRACTION100
1.7747-1.80530.27591460.20532581X-RAY DIFFRACTION100
1.8053-1.83810.25471500.19562539X-RAY DIFFRACTION100
1.8381-1.87350.21771410.20232604X-RAY DIFFRACTION100
1.8735-1.91170.29911270.25452448X-RAY DIFFRACTION96
1.9117-1.95330.40041240.30612459X-RAY DIFFRACTION95
1.9533-1.99870.20221310.17262592X-RAY DIFFRACTION100
1.9987-2.04870.2111370.16422581X-RAY DIFFRACTION99
2.0487-2.10410.3141110.22242493X-RAY DIFFRACTION95
2.1041-2.1660.17661590.15082591X-RAY DIFFRACTION100
2.166-2.23590.20361370.15982538X-RAY DIFFRACTION98
2.2359-2.31580.23841190.20442469X-RAY DIFFRACTION95
2.3158-2.40850.17161380.14242587X-RAY DIFFRACTION100
2.4085-2.51820.18161570.14182592X-RAY DIFFRACTION99
2.5182-2.65090.17141520.13422585X-RAY DIFFRACTION99
2.6509-2.8170.18841260.13892610X-RAY DIFFRACTION98
2.817-3.03450.15771440.1282601X-RAY DIFFRACTION99
3.0345-3.33980.14741540.12422612X-RAY DIFFRACTION99
3.3398-3.82290.15081230.12772596X-RAY DIFFRACTION97
3.8229-4.8160.14921320.12332657X-RAY DIFFRACTION98
4.816-51.89750.21441640.18362819X-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)
11.2129-0.50680.54421.39980.02682.5550.02370.0698-0.0245-0.0257-0.07950.11350.3831-0.01740.05120.14280.00420.00990.10350.01540.0915-18.6908-5.7094-3.2111
20.2646-0.31110.4420.9646-0.7560.8296-0.02110.01520.04710.0797-0.0447-0.0638-0.10710.00590.05410.120.02260.00320.13230.00160.0981-17.57498.455-7.1369
33.6371-0.8555-1.33810.77130.2772.3695-0.1871-0.1569-0.10780.07290.0137-0.0369-0.0435-0.07450.14250.1420.0305-0.00770.10440.03570.1046-22.377815.9142-11.7882
44.0016-0.45020.80444.27530.12142.9377-0.0943-0.0793-0.2483-0.02410.33580.54740.1926-0.6216-0.18170.1824-0.04440.03350.41140.0250.1901-34.43087.53880.4017
50.5445-0.0640.15231.3626-0.35031.2855-0.0332-0.01290.08860.068-0.0248-0.0864-0.13540.02940.07840.10460.0266-0.00310.12490.00590.09-16.06059.9698-6.8564
61.06930.3439-0.18231.8847-0.22311.7314-0.12870.1493-0.0157-0.16160.11480.1114-0.0884-0.12680.03250.1099-0.0289-0.00820.11530.0130.0921-34.8764-22.254319.393
70.87930.4508-0.36010.6839-0.17980.5456-0.07340.1765-0.0553-0.11060.07090.00380.0539-0.06020.0050.1021-0.01440.0010.1-0.0050.0761-23.7489-17.722818.7817
80.4224-0.1169-0.08251.4044-0.29370.2933-0.06110.06610.0385-0.16830.0707-0.10910.104-0.1565-0.00720.14790.00160.0120.1160.00770.074-16.3877-11.05518.0893
90.8474-1.3351-0.58392.63861.11331.3290.11330.1071-0.0634-0.2311-0.09460.0043-0.0757-0.1554-0.03930.095-0.01070.01650.1084-0.00190.0916-17.4992-8.565612.1773
102.48120.3275-0.19813.737-2.11974.7999-0.05810.11640.23340.1980.08870.4964-0.123-0.55220.02210.10390.00870.03070.1809-0.00770.2149-31.6878-2.206623.9449
110.33590.158-0.00240.84530.03550.4856-0.12370.119-0.104-0.07050.03460.05360.168-0.07610.05990.1335-0.03610.03570.1247-0.02570.0957-19.1772-16.648611.7988
121.30940.6275-0.50533.4797-0.73980.9108-0.0460.0201-0.1496-0.1318-0.0804-0.28190.0451-0.02690.11480.08420.00770.00940.087-0.00050.0895-10.9507-14.991219.0639
130.81580.7463-0.03451.05630.06330.4446-0.08510.1528-0.0376-0.16070.0994-0.0284-0.0172-0.06440.0150.1192-0.0224-0.00360.12140.00090.0899-26.0098-18.044118.1895
141.2398-0.3461-0.03220.82820.28361.6147-0.07890.02420.0676-0.0179-0.0396-0.0026-0.1191-0.03140.10990.1161-0.0212-0.01150.08110.00430.10781.761120.874726.9459
150.8130.2722-0.08770.5340.25790.4959-0.0078-0.0076-0.0024-0.01510.0309-0.0499-0.05290.0028-0.01020.1017-0.0029-0.01250.07910.00430.0882-7.128213.336928.0139
160.7004-0.0678-0.16780.97440.1730.53540.05-0.06410.0506-0.0311-0.02770.0863-0.0961-0.0131-0.01980.08880.01270.00060.089-0.00050.0922-17.557310.900936.5757
170.8723-0.31490.14610.58630.00680.0320.0899-0.01470.34470.32580.12280.4198-0.484-0.16350.07350.43120.05010.02810.14820.06890.3011-18.068727.158622.2873
181.12280.3602-0.07320.65790.27660.4916-0.0565-0.068-0.0219-0.00710.0337-0.0198-0.0280.00280.03390.08170.0069-0.00980.07120.00940.0713-10.216810.309129.6837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 185 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 34 )
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 85 )
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 112 )
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 124 )
11X-RAY DIFFRACTION11chain 'B' and (resid 125 through 141 )
12X-RAY DIFFRACTION12chain 'B' and (resid 142 through 156 )
13X-RAY DIFFRACTION13chain 'B' and (resid 157 through 185 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 34 )
15X-RAY DIFFRACTION15chain 'C' and (resid 35 through 85 )
16X-RAY DIFFRACTION16chain 'C' and (resid 86 through 112 )
17X-RAY DIFFRACTION17chain 'C' and (resid 113 through 124 )
18X-RAY DIFFRACTION18chain 'C' and (resid 125 through 185 )

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