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- PDB-3uak: Crystal Structure of De Novo designed cysteine esterase ECH14, No... -

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Basic information

Entry
Database: PDB / ID: 3uak
TitleCrystal Structure of De Novo designed cysteine esterase ECH14, Northeast Structural Genomics Consortium Target OR54
ComponentsDe Novo designed cysteine esterase ECH14
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ECH14
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.232 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Baker, D. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Computational design of catalytic dyads and oxyanion holes for ester hydrolysis.
Authors: Richter, F. / Blomberg, R. / Khare, S.D. / Kiss, G. / Kuzin, A.P. / Smith, A.J. / Gallaher, J. / Pianowski, Z. / Helgeson, R.C. / Grjasnow, A. / Xiao, R. / Seetharaman, J. / Su, M. / ...Authors: Richter, F. / Blomberg, R. / Khare, S.D. / Kiss, G. / Kuzin, A.P. / Smith, A.J. / Gallaher, J. / Pianowski, Z. / Helgeson, R.C. / Grjasnow, A. / Xiao, R. / Seetharaman, J. / Su, M. / Vorobiev, S. / Lew, S. / Forouhar, F. / Kornhaber, G.J. / Hunt, J.F. / Montelione, G.T. / Tong, L. / Houk, K.N. / Hilvert, D. / Baker, D.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De Novo designed cysteine esterase ECH14
B: De Novo designed cysteine esterase ECH14


Theoretical massNumber of molelcules
Total (without water)90,5472
Polymers90,5472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-31 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.645, 81.814, 159.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:281 or resseq 283:395 )
211chain B and (resseq 1:281 or resseq 283:395 )
Detailstrimer,152.2 kD,53.4%|aggregated,1094 kD,45.07%

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Components

#1: Protein De Novo designed cysteine esterase ECH14


Mass: 45273.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.2M MgCl2, 0.1M Bis-Tris, 25% PEG3350, sitting drop, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 27, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 26157 / % possible obs: 84.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TOI

1toi


Resolution: 3.232→19.964 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.94 / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 1420 9.97 %
Rwork0.2102 --
obs0.2179 14246 96.9 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.262 Å2 / ksol: 0.234 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8589 Å20 Å20 Å2
2---0.8303 Å2-0 Å2
3---3.6892 Å2
Refinement stepCycle: LAST / Resolution: 3.232→19.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 0 0 6144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096268
X-RAY DIFFRACTIONf_angle_d1.2048494
X-RAY DIFFRACTIONf_dihedral_angle_d17.0342278
X-RAY DIFFRACTIONf_chiral_restr0.076942
X-RAY DIFFRACTIONf_plane_restr0.0061118
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3056X-RAY DIFFRACTIONPOSITIONAL
12B3056X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2323-3.34730.43221420.3181078X-RAY DIFFRACTION86
3.3473-3.48060.36671420.30621261X-RAY DIFFRACTION97
3.4806-3.63810.35581420.27271274X-RAY DIFFRACTION98
3.6381-3.82870.34821420.25661288X-RAY DIFFRACTION99
3.8287-4.06670.30381420.23351304X-RAY DIFFRACTION99
4.0667-4.37760.28261420.19431296X-RAY DIFFRACTION99
4.3776-4.81250.25591420.15911320X-RAY DIFFRACTION99
4.8125-5.49620.21481420.16041302X-RAY DIFFRACTION98
5.4962-6.87720.28841420.19661324X-RAY DIFFRACTION98
6.8772-19.96460.22621420.18391379X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -18.8802 Å / Origin y: 29.2702 Å / Origin z: -18.682 Å
111213212223313233
T0.1662 Å20.058 Å2-0.0011 Å2-0.1443 Å20.002 Å2--0.2002 Å2
L0.6761 °20.0177 °2-0.2079 °2-0.912 °20.2467 °2--0.5786 °2
S-0.0382 Å °-0.0808 Å °0.0013 Å °-0.0478 Å °-0.0719 Å °0.0744 Å °0.1553 Å °-0.0629 Å °-0.1898 Å °
Refinement TLS groupSelection details: all
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top

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