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- PDB-3u1v: X-ray Structure of De Novo design cysteine esterase FR29, Northea... -

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Basic information

Entry
Database: PDB / ID: 3u1v
TitleX-ray Structure of De Novo design cysteine esterase FR29, Northeast Structural Genomics Consortium Target OR52
ComponentsDe Novo design cysteine esterase FR29
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / FR29 / De Novo design
Function / homologyTyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / HUPs / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.797 Å
AuthorsKuzin, A. / Su, M. / Vorobiev, S.M. / Seetharaman, J. / Patel, D. / Xiao, R. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.B. ...Kuzin, A. / Su, M. / Vorobiev, S.M. / Seetharaman, J. / Patel, D. / Xiao, R. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.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
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Sep 13, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De Novo design cysteine esterase FR29
B: De Novo design cysteine esterase FR29
C: De Novo design cysteine esterase FR29
D: De Novo design cysteine esterase FR29


Theoretical massNumber of molelcules
Total (without water)155,3884
Polymers155,3884
Non-polymers00
Water57632
1
A: De Novo design cysteine esterase FR29
C: De Novo design cysteine esterase FR29


Theoretical massNumber of molelcules
Total (without water)77,6942
Polymers77,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-19 kcal/mol
Surface area28030 Å2
MethodPISA
2
B: De Novo design cysteine esterase FR29
D: De Novo design cysteine esterase FR29


Theoretical massNumber of molelcules
Total (without water)77,6942
Polymers77,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-17 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.750, 100.764, 188.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsdimer,78.47 kD,93.2%

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Components

#1: Protein
De Novo design cysteine esterase FR29


Mass: 38846.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: macrobatch uder oil / pH: 5.6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.17M NH4Acetate, 0.085 M Na3Citrate, PEG 4000 25%, Glycerol 15%, macrobatch uder oil, temperature 293KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 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: 2.797→50 Å / Num. obs: 46680 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3FHJ

3fhj


Resolution: 2.797→42.822 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.85 / σ(F): 1.34 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2899 2116 4.99 %
Rwork0.2137 --
obs0.2175 42365 90.74 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.474 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.7648 Å2-0 Å2-0 Å2
2---8.362 Å20 Å2
3----9.4027 Å2
Refinement stepCycle: LAST / Resolution: 2.797→42.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9936 0 0 32 9968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910127
X-RAY DIFFRACTIONf_angle_d1.16713702
X-RAY DIFFRACTIONf_dihedral_angle_d17.2213830
X-RAY DIFFRACTIONf_chiral_restr0.0741540
X-RAY DIFFRACTIONf_plane_restr0.0051757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7965-2.86150.3848860.32321771X-RAY DIFFRACTION61
2.8615-2.93310.4326980.28781962X-RAY DIFFRACTION67
2.9331-3.01240.32761100.26872174X-RAY DIFFRACTION75
3.0124-3.1010.33071340.22962378X-RAY DIFFRACTION81
3.101-3.20110.30771500.22692486X-RAY DIFFRACTION86
3.2011-3.31540.28771500.22612726X-RAY DIFFRACTION94
3.3154-3.44810.30711200.23562915X-RAY DIFFRACTION98
3.4481-3.6050.33511610.23672899X-RAY DIFFRACTION99
3.605-3.79490.31851480.22022936X-RAY DIFFRACTION100
3.7949-4.03250.26841450.18632949X-RAY DIFFRACTION100
4.0325-4.34360.25331530.18692949X-RAY DIFFRACTION100
4.3436-4.78020.26061520.16492978X-RAY DIFFRACTION100
4.7802-5.47070.25921580.18262985X-RAY DIFFRACTION100
5.4707-6.88790.30811700.23293016X-RAY DIFFRACTION100
6.8879-42.82690.24881810.21583125X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 72.7875 Å / Origin y: 63.2837 Å / Origin z: 44.9955 Å
111213212223313233
T-0.0136 Å2-0.026 Å20.016 Å2--0.0491 Å20.0238 Å2--0.0015 Å2
L-0.0191 °2-0.014 °2-0.024 °2-0.0347 °20.0226 °2--0.0339 °2
S-0.0951 Å °0.021 Å °0.0345 Å °-0.0424 Å °0.0524 Å °0.0112 Å °-0.0657 Å °0.0155 Å °-0.0068 Å °
Refinement TLS groupSelection details: all

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