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- PDB-4e88: CRYSTAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, No... -

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Basic information

Entry
Database: PDB / ID: 4.0E+88
TitleCRYSTAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51
ComponentsDE NOVO DESIGNED CYSTEINE ESTERASE ECH13
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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. / Xiao, X. / Sahdev, S. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Xiao, X. / Sahdev, S. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR51
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Xiao, X. / Sahdev, S. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: 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
Revision 1.3Nov 6, 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 DESIGNED CYSTEINE ESTERASE ECH13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3022
Polymers24,2101
Non-polymers921
Water3,297183
1
A: DE NOVO DESIGNED CYSTEINE ESTERASE ECH13
hetero molecules

A: DE NOVO DESIGNED CYSTEINE ESTERASE ECH13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6044
Polymers48,4202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2630 Å2
ΔGint-9 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.994, 61.745, 59.384
Angle α, β, γ (deg.)90.000, 128.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

Detailsdimer,54.06 kD,98.7%

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Components

#1: Protein DE NOVO DESIGNED CYSTEINE ESTERASE ECH13


Mass: 24209.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#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
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: 2.59 Å3/Da / Density % sol: 52.53 %
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:100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M REMARK 280 ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M REMARK 280 NH4F, 20% PEG3350, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M , 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 % / Biso Wilson estimate: 28.24 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.9

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MIR
Starting model: pdb entry 3U13

3u13


Resolution: 2→23.091 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.866 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 828 5.07 %random
Rwork0.178 ---
obs0.18 16344 97.27 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.488 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 84.78 Å2 / Biso mean: 33.286 Å2 / Biso min: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å21.933 Å2
2--6.468 Å2-0 Å2
3----7.078 Å2
Refinement stepCycle: LAST / Resolution: 2→23.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 6 183 1775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071677
X-RAY DIFFRACTIONf_angle_d1.0732273
X-RAY DIFFRACTIONf_chiral_restr0.077235
X-RAY DIFFRACTIONf_plane_restr0.004300
X-RAY DIFFRACTIONf_dihedral_angle_d12.511644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.1250.3011180.252239235785
2.125-2.2890.2381440.1812599274399
2.289-2.520.221320.1726602792100
2.52-2.8840.2381340.18626542788100
2.884-3.6310.2231470.18726552802100
3.631-23.0920.1831530.1627092862100
Refinement TLS params.Method: refined / Origin x: 10.9111 Å / Origin y: -31.222 Å / Origin z: -10.3695 Å
111213212223313233
T0.1149 Å20.0021 Å20.0191 Å2-0.1876 Å20.0021 Å2--0.1712 Å2
L1.3812 °20.0949 °2-0.3615 °2-2.0278 °2-1.1295 °2--3.7112 °2
S0.0231 Å °0.1341 Å °0.0017 Å °-0.0559 Å °0.0858 Å °0.1192 Å °-0.0043 Å °-0.4454 Å °-0.088 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 197
2X-RAY DIFFRACTION1allA1 - 301
3X-RAY DIFFRACTION1all1 - 183

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