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- PDB-5tvv: Computationally Designed Fentanyl Binder - Fen49* Apo -

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Basic information

Entry
Database: PDB / ID: 5tvv
TitleComputationally Designed Fentanyl Binder - Fen49* Apo
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / Fentanyl Binder / Computational Design
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: 1.79 Å
AuthorsBick, M.J. / Greisen, P.J. / Morey, K.J. / Antunes, A.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)HDTRA1-11-1-0041 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 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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)61,4176
Polymers61,3003
Non-polymers1173
Water6,612367
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4722
Polymers20,4331
Non-polymers391
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)20,4722
Polymers20,4331
Non-polymers391
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)20,4722
Polymers20,4331
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.760, 73.259, 137.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Mutation: Y88A
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 0.976246 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2015
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976246 Å / Relative weight: 1
ReflectionResolution: 1.79→43.861 Å / Num. obs: 52362 / % possible obs: 98.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 18.53 Å2 / Rmerge(I) obs: 0.11 / Net I/av σ(I): 15.135 / Net I/σ(I): 13.528
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Diffraction-ID% possible allRmerge(I) obs
1.79-1.855.91.5380.573192.8
1.85-1.937.22.5280.801196.70.778
1.93-2.027.84.0120.9198.50.545
2.02-2.1285.5620.94198.90.4
2.12-2.2687.5660.964199.30.288
2.26-2.438.19.4540.978199.50.232
2.43-2.678.112.010.986199.70.177
2.67-3.068.116.6670.993199.60.12
3.06-3.868.124.3950.998199.90.06
3.86-508.551.553111000.031

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.47 Å43.86 Å
Translation6.47 Å43.86 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
Coot0.8model building
PHENIXdev_2313refinement
PDB_EXTRACT3.2data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QZ3

2qz3


Resolution: 1.79→43.861 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.79
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
Rfree0.2246 2660 5.09 %
Rwork0.2039 --
obs0.2049 52283 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.76 Å2 / Biso mean: 28.507 Å2 / Biso min: 7.74 Å2
Refinement stepCycle: final / Resolution: 1.79→43.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 3 370 4579
Biso mean--26.81 32.91 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054507
X-RAY DIFFRACTIONf_angle_d0.7146218
X-RAY DIFFRACTIONf_chiral_restr0.052654
X-RAY DIFFRACTIONf_plane_restr0.004794
X-RAY DIFFRACTIONf_dihedral_angle_d8.7022440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7877-1.82020.29831270.32482271239887
1.8202-1.85520.25851330.29052484261795
1.8552-1.89310.26781420.26262514265696
1.8931-1.93430.28031430.24522540268398
1.9343-1.97930.23421340.21952595272998
1.9793-2.02880.23551470.23092604275199
2.0288-2.08360.25931180.22812613273199
2.0836-2.14490.22911450.21712590273599
2.1449-2.21420.2281350.21332600273599
2.2142-2.29330.27111420.20062648279099
2.2933-2.38510.24951300.19722619274999
2.3851-2.49370.25131290.206426492778100
2.4937-2.62510.26191180.201826672785100
2.6251-2.78960.23121630.197326342797100
2.7896-3.00490.21161570.184126332790100
3.0049-3.30720.21661330.174326852818100
3.3072-3.78550.16351610.170426792840100
3.7855-4.76840.17951600.171627222882100
4.7684-43.87410.26471430.234328763019100
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)
11.9175-1.22160.80933.696-0.07213.6803-0.2795-0.45620.01910.20630.19950.2222-0.0183-0.44440.02420.14650.1046-0.01070.2537-0.00330.1747-7.4266-14.2785-19.2916
22.0361-1.10010.08671.70990.10971.8231-0.2072-0.36080.08990.16690.1350.0397-0.1683-0.18030.02250.12090.055-0.0150.1778-0.01670.10183.7368-18.5591-18.7112
31.3594-2.2527-0.49144.8708-0.8922.7132-0.3291-0.4173-0.18370.46890.34970.3786-0.0319-0.23470.03250.23080.0577-0.00270.25430.04530.168611.2092-25.6495-8.0892
44.6462.77361.79777.30792.28693.2883-0.0003-0.7291-0.23680.3632-0.1622-0.10080.118-0.5140.11380.11610.05160.02520.18650.04120.10489.9113-28.56-12.5559
51.8271-1.3140.05132.1442-0.24981.1852-0.0946-0.41-0.14550.15540.080.1498-0.0416-0.18550.02340.09130.05640.02680.2020.01630.13013.3591-25.441-17.0045
63.5324-1.92621.06373.0896-0.39432.5064-0.163-0.07160.104-0.2080.0749-0.2821-0.27030.0550.11350.0824-0.0083-0.00920.1298-0.00450.133116.7345-21.5387-18.8739
72.045-1.0209-0.12352.15790.48931.1541-0.1653-0.27790.10610.18040.13850.0186-0.0938-0.21120.01040.11970.0497-0.01530.1842-0.00940.09742.0072-18.4595-18.8159
82.4388-1.25270.84042.8741-0.66313.1348-0.0671-0.0381-0.15010.211-0.1046-0.0460.2016-0.15540.11470.1757-0.02670.00450.1567-0.02570.1371-28.3573-21.0667-44.7718
91.49220.0664-0.24561.05710.25711.2749-0.0274-0.1098-0.12160.1463-0.00640.02720.186-0.04330.04170.1345-0.02290.00520.1040.0070.0974-22.7424-14.6707-39.9691
105.3646-1.31691.31091.4615-0.62661.0748-0.1303-0.1255-0.0950.2780.0451-0.17740.0785-0.07180.10620.21370.021-0.00750.1496-0.02080.1008-11.2103-9.4673-30.2715
115.2588-1.8113-0.07063.66160.973.9269-0.0729-0.0776-0.32290.3090.0589-0.0340.4581-0.0363-0.00250.1681-0.0021-0.02910.13890.01830.1378-9.8123-11.6432-33.9187
120.59340.164-0.58830.4705-0.20070.59270.0539-0.0286-0.85680.56170.3556-1.08780.83050.4172-0.11490.47480.0773-0.14490.2572-0.07320.576-10.2557-26.948-45.5203
131.96850.66340.06491.83810.61621.6347-0.0437-0.04970.01270.07810.0725-0.17270.13550.0987-0.04260.09670.0175-0.01450.1080.00610.1099-14.1521-7.4796-39.6016
142.25961.0177-0.24191.91710.1932.07560.0309-0.2818-0.14380.2967-0.03750.02630.3876-0.00120.04920.1763-0.01920.00430.1494-0.00330.1147-26.1437-16.0144-37.9159
153.5236-0.55251.21174.5697-0.17075.56320.2701-0.0212-0.54560.07990.28271.06460.7478-0.6348-0.46950.3151-0.0918-0.1710.29810.08890.3679-20.1145-4.39430.0423
162.2869-1.50841.51073.6176-1.8924.01250.7160.0451-0.9207-0.8597-0.07740.46640.86660.3094-0.0420.43880.3165-0.38670.4301-0.05130.3814-16.8581-6.8161-6.2287
173.7079-1.51521.93253.9865-2.34725.84130.35930.29120.03050.4082-0.0794-0.0809-0.46540.0005-0.05370.320.06090.01570.24050.04750.1862-16.63026.2585-4.2298
183.2203-2.5012.43024.2902-0.93863.8381-0.18410.20410.03960.511-0.139-0.1358-0.25560.5570.18750.26960.0083-0.02050.28490.09070.1954-19.490315.4867-14.2949
190.5603-1.2356-0.31634.5862-1.53912.8544-0.2752-0.5478-0.58420.3640.78651.2804-0.15-1.3605-0.43960.70640.08580.38680.57720.23090.7716-33.1088.44851.2824
203.244-0.17271.83222.6931-2.22254.96630.0340.26170.07120.5482-0.0413-0.1878-0.65280.4477-0.02970.39360.0227-0.02470.2809-0.0020.1925-15.29449.738-6.2454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )A1 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 85 )A35 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 102 )A86 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 112 )A103 - 112
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 141 )A113 - 141
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 156 )A142 - 156
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 185 )A157 - 185
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 20 )B1 - 20
9X-RAY DIFFRACTION9chain 'B' and (resid 21 through 85 )B21 - 85
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 102 )B86 - 102
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 112 )B103 - 112
12X-RAY DIFFRACTION12chain 'B' and (resid 113 through 124 )B113 - 124
13X-RAY DIFFRACTION13chain 'B' and (resid 125 through 166 )B125 - 166
14X-RAY DIFFRACTION14chain 'B' and (resid 167 through 185 )B167 - 185
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 20 )C2 - 20
16X-RAY DIFFRACTION16chain 'C' and (resid 21 through 34 )C21 - 34
17X-RAY DIFFRACTION17chain 'C' and (resid 35 through 85 )C35 - 85
18X-RAY DIFFRACTION18chain 'C' and (resid 86 through 112 )C86 - 112
19X-RAY DIFFRACTION19chain 'C' and (resid 113 through 124 )C113 - 124
20X-RAY DIFFRACTION20chain 'C' and (resid 125 through 185 )C125 - 185

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