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- PDB-3u1o: THREE DIMENSIONAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE... -

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Entry
Database: PDB / ID: 3u1o
TitleTHREE DIMENSIONAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH19, Northeast Structural Genomics Consortium Target OR49
ComponentsDe Novo design cysteine esterase ECH19
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ECH19
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.494 Å
AuthorsKuzin, A. / Su, M. / Lew, S. / Forouhar, F. / Seetharaman, J. / Daya, P. / Xiao, R. / Ciccosanti, C. / Richter, F. / Everett, J.K. ...Kuzin, A. / Su, M. / Lew, S. / Forouhar, F. / Seetharaman, J. / Daya, P. / 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 1.0Oct 26, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De Novo design cysteine esterase ECH19
B: De Novo design cysteine esterase ECH19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,77112
Polymers97,1032
Non-polymers66810
Water7,909439
1
A: De Novo design cysteine esterase ECH19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1019
Polymers48,5521
Non-polymers5498
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De Novo design cysteine esterase ECH19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6713
Polymers48,5521
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.135, 129.200, 72.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

Details45.86 kD, probability=93.8%

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Components

#1: Protein De Novo design cysteine esterase ECH19


Mass: 48551.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 277 K / Method: macro batch under oil / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: Lithium sulfate monohydrate (Li2So4*H2O) - 0.1M, Bis-Tris propane - 0.1M, PEG 20000 24% (w/v), ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: Lithium sulfate monohydrate (Li2So4*H2O) - 0.1M, Bis-Tris propane - 0.1M, PEG 20000 24% (w/v), macro batch under oil, temperature 277K

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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: Jun 22, 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: 2.494→50 Å / Num. obs: 36229 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2UVJ

2uvj


Resolution: 2.494→35.027 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.85 / σ(F): 1.34 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 1802 4.99 %
Rwork0.2013 --
obs0.2043 36117 99.57 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.816 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5623 Å20 Å2-0 Å2
2--0.6285 Å20 Å2
3----1.1908 Å2
Refinement stepCycle: LAST / Resolution: 2.494→35.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 34 439 7029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086798
X-RAY DIFFRACTIONf_angle_d1.1799240
X-RAY DIFFRACTIONf_dihedral_angle_d16.1832468
X-RAY DIFFRACTIONf_chiral_restr0.081978
X-RAY DIFFRACTIONf_plane_restr0.0051169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4944-2.56190.3891320.27052524X-RAY DIFFRACTION97
2.5619-2.63720.3081480.23012576X-RAY DIFFRACTION100
2.6372-2.72230.32191300.22852627X-RAY DIFFRACTION100
2.7223-2.81960.29151330.23072614X-RAY DIFFRACTION100
2.8196-2.93240.31761310.20782628X-RAY DIFFRACTION100
2.9324-3.06580.27261300.21672630X-RAY DIFFRACTION100
3.0658-3.22730.27661300.21112638X-RAY DIFFRACTION100
3.2273-3.42940.23771270.21562638X-RAY DIFFRACTION100
3.4294-3.69390.21021410.22636X-RAY DIFFRACTION100
3.6939-4.06510.241610.17082632X-RAY DIFFRACTION100
4.0651-4.65220.21731160.14782680X-RAY DIFFRACTION100
4.6522-5.85680.22781520.18192698X-RAY DIFFRACTION100
5.8568-35.03040.27631710.21242794X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 50.9315 Å / Origin y: 56.6045 Å / Origin z: 23.5327 Å
111213212223313233
T0.1106 Å20.0074 Å20.012 Å2-0.1004 Å20.0058 Å2--0.0972 Å2
L0.049 °20.0148 °20.0212 °2-0.0642 °20.0184 °2--0.0365 °2
S-0.0162 Å °0.0051 Å °0.0129 Å °-0.0016 Å °0.006 Å °0.0128 Å °0.001 Å °0.0018 Å °0.0119 Å °
Refinement TLS groupSelection details: all

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