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- PDB-4etk: Crystal Structure of E6A/L130D/A155H variant of de novo designed ... -

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Basic information

Entry
Database: PDB / ID: 4etk
TitleCrystal Structure of E6A/L130D/A155H variant of de novo designed serine hydrolase, Northeast Structural Genomics Consortium (NESG) Target OR186
ComponentsDe novo designed serine hydrolase
KeywordsHYDROLASE / 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
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
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
Revision 1.5Nov 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 serine hydrolase
B: De novo designed serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5833
Polymers35,5602
Non-polymers231
Water1629
1
A: De novo designed serine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8032
Polymers17,7801
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: De novo designed serine hydrolase


Theoretical massNumber of molelcules
Total (without water)17,7801
Polymers17,7801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.196, 133.661, 29.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsmonomer,16.94 kD,91.9%, dimer,31.24 kD,5.85%

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Components

#1: Protein De novo designed serine hydrolase


Mass: 17779.996 Da / Num. of mol.: 2 / Mutation: E6A, L130D, A155H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Plasmid: pet29b / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.2M Mg-acetate, 20% PEG 3350, microbatch under oil, temperature 293KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97906 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 8, 2012 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97906 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 11430 / % possible obs: 85.4 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 5.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V45

3v45


Resolution: 2.7→38.709 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.812 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 545 4.79 %random
Rwork0.1876 ---
obs0.188 11385 87.06 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.88 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 108.41 Å2 / Biso mean: 25.07 Å2 / Biso min: 5.27 Å2
Baniso -1Baniso -2Baniso -3
1-17.336 Å20 Å20 Å2
2---9.087 Å20 Å2
3----8.248 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 1 9 2469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072443
X-RAY DIFFRACTIONf_angle_d1.0763297
X-RAY DIFFRACTIONf_chiral_restr0.067388
X-RAY DIFFRACTIONf_plane_restr0.004432
X-RAY DIFFRACTIONf_dihedral_angle_d15.292892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.394-2.6350.333890.2191980206965
2.635-3.0160.2821380.1812554269283
3.016-3.7990.2251680.1663040320899
3.799-38.7140.2491500.18332663416100
Refinement TLS params.Method: refined / Origin x: 16.5204 Å / Origin y: 63.2948 Å / Origin z: 9.2632 Å
111213212223313233
T0.0625 Å20.0192 Å2-0.0053 Å2-0.0767 Å2-0.0011 Å2--0.0573 Å2
L0.0589 °20.1094 °2-0.0212 °2-0.7253 °2-0.0074 °2--0.1405 °2
S-0.0153 Å °0.0053 Å °-0.0193 Å °0.014 Å °0.0143 Å °-0.0294 Å °0.0039 Å °0.0529 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 167
2X-RAY DIFFRACTION1allB2 - 161
3X-RAY DIFFRACTION1allA - B1 - 206
4X-RAY DIFFRACTION1allB1 - 208
5X-RAY DIFFRACTION1allA1 - 213
6X-RAY DIFFRACTION1allB1 - 215
7X-RAY DIFFRACTION1allB - A2 - 347
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param
X-RAY DIFFRACTION6acy.par
X-RAY DIFFRACTION7peg.par

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