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- PDB-3u19: CRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED ... -

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Basic information

Entry
Database: PDB / ID: 3u19
TitleCRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51
Componentsartificial protein OR51
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ECH13 / coumarin
Function / homologyDeoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 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: To be Published
Title: CRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51
Authors: 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.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 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: artificial protein OR51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4182
Polymers24,3261
Non-polymers921
Water3,297183
1
A: artificial protein OR51
hetero molecules

A: artificial protein OR51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8364
Polymers48,6522
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2550 Å2
ΔGint-10 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.994, 61.745, 59.384
Angle α, β, γ (deg.)90.00, 128.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

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

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Components

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


Mass: 24326.154 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)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.2M NH4F, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 16356 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.1 / % possible all: 78.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MIR
Starting model: pdb entry 1Q92

1q92


Resolution: 2→23.091 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.49 / σ(F): 1.38 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 828 5.07 %
Rwork0.1767 --
obs0.1785 16344 97.27 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.074 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6883 Å20 Å22.0341 Å2
2--6.4572 Å2-0 Å2
3----7.1455 Å2
Refinement stepCycle: LAST / Resolution: 2→23.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 6 183 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071687
X-RAY DIFFRACTIONf_angle_d1.062287
X-RAY DIFFRACTIONf_dihedral_angle_d12.682644
X-RAY DIFFRACTIONf_chiral_restr0.075237
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.12540.30181180.25542239X-RAY DIFFRACTION85
2.1254-2.28930.23511440.18162599X-RAY DIFFRACTION99
2.2893-2.51950.21871320.16692660X-RAY DIFFRACTION100
2.5195-2.88350.23991340.1832654X-RAY DIFFRACTION100
2.8835-3.63060.22351470.18742655X-RAY DIFFRACTION100
3.6306-23.09220.1751530.15772709X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.9422 Å / Origin y: -31.2562 Å / Origin z: -10.3519 Å
111213212223313233
T0.1127 Å20.0029 Å20.0161 Å2-0.1876 Å20.0053 Å2--0.1695 Å2
L1.3273 °20.1421 °2-0.4273 °2-1.8989 °2-0.9527 °2--3.5994 °2
S0.0243 Å °0.1376 Å °0.0087 Å °-0.0673 Å °0.0772 Å °0.1003 Å °0.0064 Å °-0.4381 Å °-0.0843 Å °
Refinement TLS groupSelection details: all

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