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- PDB-4jvv: Crystal structure of the evolved variant of the computationally d... -

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Basic information

Entry
Database: PDB / ID: 4jvv
TitleCrystal structure of the evolved variant of the computationally designed serine hydrolase, OSH55.4_H1, covalently bound with diisopropyl fluorophosphate (DFP), Northeast Structural Genomics Consortium (NESG) Target OR273
Componentsevolved variant of the computationally designed serine hydrolase
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) Target OR273 / diisopropyl fluorophosphate / OSH55.4_H1
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: 2.288 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 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 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: evolved variant of the computationally designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)16,9951
Polymers16,9951
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.153, 67.668, 37.537
Angle α, β, γ (deg.)90.000, 94.350, 90.000
Int Tables number5
Space group name H-MC121
Detailsmonomer,18.7 kD,91.8%

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Components

#1: Protein evolved variant of the computationally designed serine hydrolase


Mass: 16995.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21_NESG / Cell line (production host): BL21(DE3) + Magic / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 10
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: NH4Cl 0.1M, CAPS 0.1M, PEG400 40%, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97894 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.288→50 Å / Num. obs: 7903 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 20.09 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 23

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1296refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JCA

4jca


Resolution: 2.288→26.58 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.816 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.244 370 4.87 %random
Rwork0.192 ---
obs0.195 7594 95.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.09 Å2 / Biso mean: 31.035 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: LAST / Resolution: 2.288→26.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 0 0 93 1270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071203
X-RAY DIFFRACTIONf_angle_d1.1931629
X-RAY DIFFRACTIONf_chiral_restr0.08185
X-RAY DIFFRACTIONf_plane_restr0.005211
X-RAY DIFFRACTIONf_dihedral_angle_d14.11451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.288-2.6190.3091140.2142226234089
2.619-3.2980.3071280.20525192647100
3.298-26.5820.1891280.1772479260797
Refinement TLS params.Method: refined / Origin x: 12.1245 Å / Origin y: -1.0919 Å / Origin z: 15.5821 Å
111213212223313233
T0.1914 Å20.0067 Å20.0096 Å2-0.2175 Å20.0198 Å2--0.1488 Å2
L2.3047 °20.1142 °20.266 °2-5.3235 °20.8697 °2--0.8947 °2
S0.0369 Å °0.023 Å °-0.0918 Å °-0.4521 Å °-0.0257 Å °0.0147 Å °-0.0567 Å °0.0293 Å °0.0065 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 159
2X-RAY DIFFRACTION1allA1 - 293

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