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- PDB-3u13: Crystal Structure of de Novo design of cystein esterase ECH13 at ... -

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Basic information

Entry
Database: PDB / ID: 3u13
TitleCrystal Structure of de Novo design of cystein esterase ECH13 at the resolution 1.6A, Northeast Structural Genomics Consortium Target OR51
Componentsartificial protein OR51Artificiality
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ECH13
Function / homology
Function and homology information


Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kohan, E. / Richter, F. / Everett, J.K. / Acton, T.B. / Baker, D. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kohan, E. / 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 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 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 / pdbx_struct_special_symmetry / 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_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.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_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_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

Downloads & links

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Assembly

Deposited unit
A: artificial protein OR51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5376
Polymers24,1941
Non-polymers3435
Water4,468248
1
A: artificial protein OR51
hetero molecules

A: artificial protein OR51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,07512
Polymers48,3882
Non-polymers68710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3330 Å2
ΔGint-62 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.436, 73.436, 105.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-441-

HOH

Detailsauthors indicate the biological unit as a trimer of 61.03 kD at 96.3%

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Components

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Protein , 1 types, 1 molecules A

#1: Protein artificial protein OR51 / Artificiality / 5' / 3'-nucleotidase / mitochondrial / Deoxy-5'-nucleotidase 2 / dNT-2


Mass: 24193.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b+ / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 253 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1M NaHPO4, 0.1M MES, PEG 20K 12%, VAPOR DIFFUSION, SITTING DROP, temperature 277KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 12, 2011 / Details: Rh coated flat mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 72527 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 48.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1Q92

1q92


Resolution: 1.6→29.039 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.35 / σ(F): 1.35 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 1932 5 %
Rwork0.1802 --
obs0.1808 38618 99.92 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.229 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.708 Å2-0 Å20 Å2
2---0.708 Å2-0 Å2
3---1.4161 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 19 248 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081688
X-RAY DIFFRACTIONf_angle_d1.2142295
X-RAY DIFFRACTIONf_dihedral_angle_d11.839645
X-RAY DIFFRACTIONf_chiral_restr0.082240
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5995-1.63950.24021400.24422557X-RAY DIFFRACTION100
1.6395-1.68380.24411350.21912570X-RAY DIFFRACTION100
1.6838-1.73330.20951450.19632572X-RAY DIFFRACTION100
1.7333-1.78930.24951310.18432590X-RAY DIFFRACTION100
1.7893-1.85320.21021180.17772585X-RAY DIFFRACTION100
1.8532-1.92740.18821570.16462575X-RAY DIFFRACTION100
1.9274-2.01510.19371550.16932568X-RAY DIFFRACTION100
2.0151-2.12130.16841390.16542601X-RAY DIFFRACTION100
2.1213-2.25420.17971200.16952630X-RAY DIFFRACTION100
2.2542-2.42810.21861380.17272618X-RAY DIFFRACTION100
2.4281-2.67230.19141340.18572648X-RAY DIFFRACTION100
2.6723-3.05870.21181330.18172665X-RAY DIFFRACTION100
3.0587-3.85220.17041490.16562678X-RAY DIFFRACTION100
3.8522-29.04340.18411380.19182829X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.7591 Å / Origin y: 20.2865 Å / Origin z: 18.8419 Å
111213212223313233
T0.1015 Å2-0.0142 Å20.0298 Å2-0.1158 Å2-0.0029 Å2--0.0887 Å2
L2.2193 °2-0.172 °2-0.4426 °2-1.6243 °2-0.3777 °2--1.1478 °2
S0.0379 Å °-0.0624 Å °0.0949 Å °0.0156 Å °-0.013 Å °-0.1523 Å °-0.1052 Å °0.0698 Å °-0.0227 Å °
Refinement TLS groupSelection details: all

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