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- PDB-4j4z: Crystal structure of the improved variant of the evolved serine h... -

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Basic information

Entry
Database: PDB / ID: 4j4z
TitleCrystal structure of the improved variant of the evolved serine hydrolase, OSH55.4_H1.2, bond with sulfate ion in the active site, Northeast Structural Genomics Consortium (NESG) Target OR301
ComponentsDesigned serine hydrolase variant OSH55.4_H1.2
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) Target OR301 / OSH55.4_H1.2 / serine hydrolase
Function / homologyLeucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsKuzin, A.P. / Lew, S. / Rajagopalan, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. ...Kuzin, A.P. / Lew, S. / Rajagopalan, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the improved variant of the evolved serine hydrolase, OSH55.4_H1.2, bond with sulfate ion in the active site, Northeast Structural Genomics Consortium (NESG) Target OR301
Authors: Kuzin, A.P. / Lew, S. / Rajagopalan, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Designed serine hydrolase variant OSH55.4_H1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7677
Polymers18,0181
Non-polymers7496
Water3,297183
1


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

A: Designed serine hydrolase variant OSH55.4_H1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,53414
Polymers36,0362
Non-polymers1,49812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area4620 Å2
ΔGint-42 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.906, 66.771, 38.102
Angle α, β, γ (deg.)90.00, 100.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Designed serine hydrolase variant OSH55.4_H1.2


Mass: 18018.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: ammonium sulfate 1M, HEPES 0.1M, PEG8000 0.5%, micro batch under oil, temperature 277K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2012
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: 1.26→47.93 Å / Num. obs: 90701 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 9.86 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→33.386 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.904 / SU ML: 0.12 / σ(F): 1.26 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 4600 5.07 %
Rwork0.169 --
obs0.17 90701 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.54 Å2 / Biso mean: 14.55 Å2 / Biso min: 4.15 Å2
Refinement stepCycle: LAST / Resolution: 1.26→33.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 40 183 1426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051354
X-RAY DIFFRACTIONf_angle_d1.1231847
X-RAY DIFFRACTIONf_chiral_restr0.076205
X-RAY DIFFRACTIONf_plane_restr0.006239
X-RAY DIFFRACTIONf_dihedral_angle_d14.591517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.26-1.2740.2821650.3012618278390
1.274-1.2890.3181540.2962739289396
1.289-1.3050.2421640.262908307298
1.305-1.3210.2751330.2582823295699
1.321-1.3390.2421350.2192885302098
1.339-1.3570.2491400.2192866300699
1.357-1.3770.2441530.2082880303399
1.377-1.3970.2251730.2042880305399
1.397-1.4190.2111530.1932871302499
1.419-1.4420.211760.1942834301099
1.442-1.4670.1871700.1862894306499
1.467-1.4940.21360.1822831296799
1.494-1.5220.171410.1772932307399
1.522-1.5540.1991700.1612900307099
1.554-1.5870.1691490.15628502999100
1.587-1.6240.1941520.14828633015100
1.624-1.6650.1781890.15229343123100
1.665-1.710.1741440.1528783022100
1.71-1.760.1511480.1528623010100
1.76-1.8170.1871860.15529003086100
1.817-1.8820.1731420.1628803022100
1.882-1.9570.1591360.1622878301499
1.957-2.0460.2161630.15429173080100
2.046-2.1540.1331360.14929023038100
2.154-2.2890.1861510.1612884303599
2.289-2.4660.181480.15728803028100
2.466-2.7140.1621370.16729423079100
2.714-3.1060.1641300.16828963026100
3.106-3.9130.1461450.15729113056100
3.913-33.3970.1731810.1572863304499
Refinement TLS params.Method: refined / Origin x: 14.6173 Å / Origin y: 44.4878 Å / Origin z: 34.293 Å
111213212223313233
T0.039 Å20.005 Å2-0.0004 Å2-0.0633 Å2-0.0028 Å2--0.0571 Å2
L0.8473 °2-0.2601 °20.0833 °2-1.1769 °2-0.102 °2--0.54 °2
S0.0119 Å °0.0108 Å °0.0491 Å °-0.0408 Å °-0.0106 Å °0.0895 Å °-0.0443 Å °-0.0634 Å °0.0047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 162
2X-RAY DIFFRACTION1allA1 - 484
3X-RAY DIFFRACTION1allA1 - 202
4X-RAY DIFFRACTION1allA1 - 205
5X-RAY DIFFRACTION1allA1 - 206

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