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- PDB-4jll: Crystal Structure of the evolved variant of the computationally d... -

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Basic information

Entry
Database: PDB / ID: 4jll
TitleCrystal Structure of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1 covalently bound with FP-alkyne, Northeast Structural Genomics Consortium (NESG) Target OR273
ComponentsEvolved variant of computationally designed serine hydrolase OSH55.4_H1
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) / OSH55.4_H1 / ser hydrolase
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Chem-SEF
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Tong, S. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. ...Kuzin, A. / Lew, S. / Rajagopalan, S. / Seetharaman, J. / Tong, S. / Everett, J.K. / Acton, T.B. / Baker, D. / 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
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Evolved variant of computationally designed serine hydrolase OSH55.4_H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,85011
Polymers17,8081
Non-polymers1,04210
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Evolved variant of computationally designed serine hydrolase OSH55.4_H1
hetero molecules

A: Evolved variant of computationally designed serine hydrolase OSH55.4_H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,70022
Polymers35,6162
Non-polymers2,08320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5790 Å2
ΔGint-8 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.846, 66.977, 37.911
Angle α, β, γ (deg.)90.00, 100.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

Detailsmonomer,18.7 kD,91.8%

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Evolved variant of computationally designed serine hydrolase OSH55.4_H1


Mass: 17808.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic

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Non-polymers , 6 types, 208 molecules

#2: Chemical ChemComp-SEF / ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate


Mass: 405.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H37FNO4P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 4.2
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:RbCl 0.1M, Sodium Citrate 0.1M, PEG1000 40%, , microbatch under oil, temperature 277K

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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: Jul 26, 2012 / Details: mirrors
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: 1.36→50 Å / Num. obs: 32937 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 10.98 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 43.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V45

3v45


Resolution: 1.36→33.488 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.161 1670 5.07 %random
Rwork0.145 ---
obs0.145 32931 90.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.48 Å2 / Biso mean: 16.414 Å2 / Biso min: 4.92 Å2
Refinement stepCycle: LAST / Resolution: 1.36→33.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 66 198 1458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081337
X-RAY DIFFRACTIONf_angle_d1.0821789
X-RAY DIFFRACTIONf_chiral_restr0.075198
X-RAY DIFFRACTIONf_plane_restr0.005228
X-RAY DIFFRACTIONf_dihedral_angle_d15.58524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.358-1.3980.182620.1661428149049
1.398-1.4430.217850.1541824190964
1.443-1.4940.1541060.1462218232477
1.494-1.5540.1561450.1392683282893
1.554-1.6250.1391560.13628583014100
1.625-1.710.1521630.13928883051100
1.71-1.8170.1621370.1428743011100
1.817-1.9580.1641590.14228793038100
1.958-2.1550.1551610.13529013062100
2.155-2.4670.1691560.14528973053100
2.467-3.1070.1521610.14928983059100
3.107-33.4990.1661790.14929133092100
Refinement TLS params.Method: refined / Origin x: -13.22 Å / Origin y: 1.6786 Å / Origin z: -3.6913 Å
111213212223313233
T0.0493 Å20.003 Å2-0.0059 Å2-0.0767 Å2-0.0038 Å2--0.0695 Å2
L0.9948 °2-0.2243 °2-0.0945 °2-1.2663 °2-0.1076 °2--0.8209 °2
S0.0478 Å °0.0331 Å °0.0657 Å °-0.0586 Å °-0.0131 Å °0.111 Å °-0.0483 Å °-0.0638 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 162
2X-RAY DIFFRACTION1allA1 - 202
3X-RAY DIFFRACTION1allA1 - 207
4X-RAY DIFFRACTION1allA1 - 492
5X-RAY DIFFRACTION1allU1 - 6
6X-RAY DIFFRACTION1allA1 - 208
7X-RAY DIFFRACTION1allA1 - 210

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