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- PDB-7c2c: Esterase AlinE4 mutant, D162A -

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Basic information

Entry
Database: PDB / ID: 7c2c
TitleEsterase AlinE4 mutant, D162A
ComponentsSGNH-hydrolase family esterase
KeywordsHYDROLASE / esterase / SGNH-hydrolase family / marine
Function / homology
Function and homology information


phosphatidylcholine lysophospholipase activity / carboxylic ester hydrolase activity
Similarity search - Function
: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / : / SGNH-hydrolase family esterase / SGNH-hydrolase family esterase
Similarity search - Component
Biological speciesAltererythrobacter indicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsLi, Z. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: To Be Published
Title: C-terminal swapped dimers revealed a new catalytic mechanism of SGNH-hydrolase family esterases
Authors: Li, Z. / Li, J.
History
DepositionMay 7, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 20, 2020ID: 6M45
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SGNH-hydrolase family esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3248
Polymers20,6641
Non-polymers6607
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.810, 79.810, 60.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

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Components

#1: Protein SGNH-hydrolase family esterase


Mass: 20663.711 Da / Num. of mol.: 1 / Mutation: D162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Altererythrobacter indicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYH5, UniProt: A0A4P1LYH6*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 1M Sodium acetate, 100mM HEPES, pH 7.5, 50mM Cadmium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.06881 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06881 Å / Relative weight: 1
ReflectionResolution: 1.55→48.42 Å / Num. obs: 29038 / % possible obs: 99.97 % / Redundancy: 2 % / Biso Wilson estimate: 12.39 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 32.71
Reflection shellResolution: 1.55→1.64 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 4174

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: 4jgg

4jgg


Resolution: 1.55→48.42 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.7117
RfactorNum. reflection% reflection
Rfree0.1819 2000 6.89 %
Rwork0.164 --
obs0.1652 29038 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.31 Å2
Refinement stepCycle: LAST / Resolution: 1.55→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 18 188 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671562
X-RAY DIFFRACTIONf_angle_d0.81282119
X-RAY DIFFRACTIONf_chiral_restr0.0532231
X-RAY DIFFRACTIONf_plane_restr0.0057286
X-RAY DIFFRACTIONf_dihedral_angle_d19.7825601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.20211390.16271889X-RAY DIFFRACTION99.95
1.59-1.630.20921410.16521895X-RAY DIFFRACTION100
1.63-1.680.17281400.1611893X-RAY DIFFRACTION100
1.68-1.740.19041420.1661912X-RAY DIFFRACTION100
1.74-1.80.19291400.16431904X-RAY DIFFRACTION100
1.8-1.870.20341400.15891889X-RAY DIFFRACTION100
1.87-1.960.1721410.161906X-RAY DIFFRACTION100
1.96-2.060.19341420.16431931X-RAY DIFFRACTION100
2.06-2.190.18431430.15641920X-RAY DIFFRACTION100
2.19-2.360.15851420.15971929X-RAY DIFFRACTION100
2.36-2.590.19161440.17121932X-RAY DIFFRACTION99.95
2.59-2.970.19821440.17161964X-RAY DIFFRACTION100
2.97-3.740.17531470.16391971X-RAY DIFFRACTION99.91
3.74-48.420.16811550.16342103X-RAY DIFFRACTION99.87

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