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- PDB-3v45: Crystal Structure of de novo designed serine hydrolase OSH55, Nor... -

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Basic information

Entry
Database: PDB / ID: 3v45
TitleCrystal Structure of de novo designed serine hydrolase OSH55, Northeast Structural Genomics Consortium Target OR130
ComponentsSerine hydrolase OSH55
KeywordsDE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / de novo design
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Rajagopalan, S. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Rajagopalan, S. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, 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
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 OSH55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7574
Polymers17,6751
Non-polymers813
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.031, 38.115, 128.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Details17.58 kD,96.8%

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Components

#1: Protein Serine hydrolase OSH55


Mass: 17675.244 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:succinic acid 1M, Hepes 0.1M, PEG 2k 1%, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 4516 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rsym value: 0.189 / Net I/σ(I): 9.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DX6

2dx6


Resolution: 2.6→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 692 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 187 3.8 %random
Rwork0.208 ---
obs-3441 69.7 %-
Solvent computationBsol: 25.452 Å2
Displacement parametersBiso max: 123.88 Å2 / Biso mean: 36.898 Å2 / Biso min: 4.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.742 Å20 Å20 Å2
2--10.701 Å20 Å2
3----5.959 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 3 13 1250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.298
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 DIFFRACTION6Cyc.par
X-RAY DIFFRACTION7hepes.par

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