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- PDB-3tes: Crystal Structure of Tencon -

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Basic information

Entry
Database: PDB / ID: 3tes
TitleCrystal Structure of Tencon
ComponentsTenconButalbital/acetaminophen
KeywordsDE NOVO PROTEIN / Fibronectin type III domain / FN3 / consensus design
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, J. / Jacobs, S. / Teplyakov, A. / Obmolova, G. / O'Neil, K. / Gilliland, G.
CitationJournal: Protein Eng.Des.Sel. / Year: 2012
Title: Design of novel FN3 domains with high stability by a consensus sequence approach.
Authors: Jacobs, S.A. / Diem, M.D. / Luo, J. / Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. / O'Neil, K.T.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tencon
B: Tencon
C: Tencon
D: Tencon


Theoretical massNumber of molelcules
Total (without water)42,9954
Polymers42,9954
Non-polymers00
Water2,144119
1
A: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.720, 87.580, 56.220
Angle α, β, γ (deg.)90.00, 103.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tencon / Butalbital/acetaminophen


Mass: 10748.873 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 3.5
Details: 0.1 M sodium citrate, 6% PEG 4000, pH 3.5, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15396 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.078

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.56 Å / SU ML: 0.34 / σ(F): 1.39 / Phase error: 36.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 384 2.51 %Random
Rwork0.2419 ---
obs0.2432 15313 96.15 %-
all-15313 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.482 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3614 Å2-0 Å2-14.0994 Å2
2---7.2761 Å20 Å2
3---10.6375 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 0 119 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032903
X-RAY DIFFRACTIONf_angle_d0.7883951
X-RAY DIFFRACTIONf_dihedral_angle_d12.0231051
X-RAY DIFFRACTIONf_chiral_restr0.063447
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.86160.35721270.31084998X-RAY DIFFRACTION97
2.8616-3.60390.29061310.24155000X-RAY DIFFRACTION97
3.6039-26.56150.27891260.22054931X-RAY DIFFRACTION94
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)
10.04180.03950.06240.4926-0.01810.1225-0.1224-0.11050.0079-0.02550.17260.2116-0.04950.0082-0.03990.12510.01360.02750.16110.01290.1369-4.538929.58716.4562
20.1581-0.10060.17610.4791-0.04710.217-0.0855-0.06040.09690.16480.0906-0.1547-0.10460.0124-0.01690.11910.00420.0290.1609-0.02320.169113.279429.831816.3807
30.42990.0802-0.04960.192-0.00510.32520.1588-0.0582-0.13790.0705-0.10910.0157-0.0246-0.069-0.02390.1154-0.0122-0.00890.10280.00460.09493.383753.685412.4296
40.5350.12810.11680.2813-0.08530.36190.1891-0.0351-0.18390.1357-0.017-0.04750.08790.0538-0.07760.1812-0.0079-0.03780.1337-0.00950.187822.374453.583219.545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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