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- PDB-4ess: Crystal Structure of E6D/L155R variant of de novo designed serine... -

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Basic information

Entry
Database: PDB / ID: 4ess
TitleCrystal Structure of E6D/L155R variant of de novo designed serine hydrolase OSH55, Northeast Structural Genomics Consortium (NESG) Target OR187
ComponentsOR187
KeywordsDe Novo Protein / hydrolase / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) Target OR187 / OSH55 mutant E6D/L159R / serine hydrolase
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9971 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Kornhaber, K. / Kornhaber, G. / Rajagopalan, S. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Kornhaber, K. / Kornhaber, G. / Rajagopalan, S. / Baker, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Design of activated serine-containing catalytic triads with atomic-level accuracy.
Authors: Rajagopalan, S. / Wang, C. / Yu, K. / Kuzin, A.P. / Richter, F. / Lew, S. / Miklos, A.E. / Matthews, M.L. / Seetharaman, J. / Su, M. / Hunt, J.F. / Cravatt, B.F. / Baker, D.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references / Structure summary
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Apr 16, 2014Group: Database references
Revision 1.4May 14, 2014Group: Database references
Revision 1.5Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OR187


Theoretical massNumber of molelcules
Total (without water)17,7051
Polymers17,7051
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.698, 46.074, 30.179
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-295-

HOH

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Components

#1: Protein OR187


Mass: 17705.252 Da / Num. of mol.: 1 / Mutation: E6D/L159R / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 6.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution:0.1M MES, 25% PEG8K, microbatch under 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: Apr 5, 2012 / Details: mirror
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: 1.997→30 Å / Num. obs: 10472 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.1

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V45

3v45


Resolution: 1.9971→29.425 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 27.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 500 4.78 %
Rwork0.2005 --
obs0.2034 10464 99.16 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.971 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.003 Å2-0 Å2-3.0697 Å2
2--1.0673 Å2-0 Å2
3----9.0703 Å2
Refinement stepCycle: LAST / Resolution: 1.9971→29.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 95 1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071188
X-RAY DIFFRACTIONf_angle_d1.1421603
X-RAY DIFFRACTIONf_dihedral_angle_d14.152443
X-RAY DIFFRACTIONf_chiral_restr0.073190
X-RAY DIFFRACTIONf_plane_restr0.005209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9971-2.1980.24541020.2012426X-RAY DIFFRACTION97
2.198-2.51590.30181240.20492496X-RAY DIFFRACTION100
2.5159-3.16920.29161260.21312498X-RAY DIFFRACTION100
3.1692-29.42790.24081480.19222544X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.4164 Å / Origin y: 0.1439 Å / Origin z: -10.2663 Å
111213212223313233
T0.1363 Å2-0.0043 Å2-0.009 Å2-0.1604 Å2-0.0023 Å2--0.1369 Å2
L1.2688 °2-0.5937 °2-0.0056 °2-1.1646 °2-0.2116 °2--1.6452 °2
S-0.0498 Å °-0.069 Å °0.0584 Å °0.1108 Å °0.0351 Å °-0.115 Å °-0.0007 Å °0.282 Å °0.0314 Å °
Refinement TLS groupSelection details: all

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