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- PDB-4etj: Crystal Structure of E6H variant of de novo designed serine hydro... -

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Basic information

Entry
Database: PDB / ID: 4etj
TitleCrystal Structure of E6H variant of de novo designed serine hydrolase OSH55, Northeast Structural Genomics Consortium (NESG) Target OR185
ComponentsSerine hydrolase
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHORYL-HEXAETHYLENE GLYCOL
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.203 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 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8355
Polymers17,6841
Non-polymers1,1514
Water66737
1
A: Serine hydrolase
hetero molecules

A: Serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,67010
Polymers35,3692
Non-polymers2,3018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4310 Å2
ΔGint-22 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.930, 65.930, 89.260
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-201-

CL

Detailsmonomer,17.05 kD,95.7%, dimer,34.77 kD,4.68%

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine hydrolase /


Mass: 17684.277 Da / Num. of mol.: 1 / Mutation: E6H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others)

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Non-polymers , 5 types, 41 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical ChemComp-PE6 / PHOSPHORYL-HEXAETHYLENE GLYCOL


Mass: 362.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27O10P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M MgCl2, 0.1M Bis-Tris, 80% PEG400, microbatch under oil, temperature 293KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97925 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 21, 2012 / Details: MIRROR
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 19058 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.9 % / Biso Wilson estimate: 36.45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 57.6

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MIR
Starting model: 3V45

3v45


Resolution: 2.203→36.958 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 502 4.79 %
Rwork0.183 --
obs0.1849 10470 99.93 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.029 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4218 Å20 Å2-0 Å2
2--1.4218 Å2-0 Å2
3----2.8436 Å2
Refinement stepCycle: LAST / Resolution: 2.203→36.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 46 37 1297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081273
X-RAY DIFFRACTIONf_angle_d1.0851704
X-RAY DIFFRACTIONf_dihedral_angle_d17.508485
X-RAY DIFFRACTIONf_chiral_restr0.07196
X-RAY DIFFRACTIONf_plane_restr0.005217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2027-2.42430.25951200.19522426X-RAY DIFFRACTION100
2.4243-2.7750.2221340.19432437X-RAY DIFFRACTION100
2.775-3.49580.24931260.17532472X-RAY DIFFRACTION100
3.4958-36.96360.20651220.18132633X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.6904 Å / Origin y: 13.5459 Å / Origin z: 14.1463 Å
111213212223313233
T0.1942 Å20.005 Å20.01 Å2-0.294 Å20.0623 Å2--0.2653 Å2
L2.4074 °21.0594 °20.0247 °2-3.1653 °20.4689 °2--4.5167 °2
S-0.0585 Å °0.0363 Å °0.189 Å °-0.1093 Å °0.0609 Å °0.0638 Å °-0.0745 Å °0.3546 Å °-0.0012 Å °
Refinement TLS groupSelection details: all

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