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- PDB-7c2d: Esterase AlinE4 mutant-S13A -

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Basic information

Entry
Database: PDB / ID: 7c2d
TitleEsterase AlinE4 mutant-S13A
ComponentsSGNH-hydrolase family esterase
KeywordsHYDROLASE / esterase / SGNH-hydrolase family / marine
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / phosphatidylcholine lysophospholipase activity / ACETATE ION / : / SGNH-hydrolase family esterase / SGNH-hydrolase family esterase
Function and homology information
Biological speciesAltererythrobacter indicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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: 6M46
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.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

Downloads & links

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Assembly

Deposited unit
A: SGNH-hydrolase family esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4258
Polymers20,6921
Non-polymers7347
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.810, 79.810, 60.820
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-373-

HOH

21A-442-

HOH

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Components

#1: Protein SGNH-hydrolase family esterase / AlinE4


Mass: 20691.721 Da / Num. of mol.: 1 / Mutation: S13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Altererythrobacter indicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYH5, UniProt: A0A4P1LYH7*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
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: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→39.9 Å / Num. obs: 20419 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.9
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.104 / Num. unique obs: 2929

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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: 1.75→39.9 Å / SU ML: 0.1578 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.898
RfactorNum. reflection% reflection
Rfree0.2049 1053 5.17 %
Rwork0.1707 --
obs0.1724 20382 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 10 151 1599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591535
X-RAY DIFFRACTIONf_angle_d0.78142084
X-RAY DIFFRACTIONf_chiral_restr0.0566229
X-RAY DIFFRACTIONf_plane_restr0.0057282
X-RAY DIFFRACTIONf_dihedral_angle_d21.6148591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.830.25181290.19582366X-RAY DIFFRACTION100
1.83-1.930.23291220.16172363X-RAY DIFFRACTION100
1.93-2.050.19611500.16342371X-RAY DIFFRACTION100
2.05-2.20.21911330.15592371X-RAY DIFFRACTION100
2.2-2.430.19041250.15992397X-RAY DIFFRACTION100
2.43-2.780.20051260.17332422X-RAY DIFFRACTION100
2.78-3.50.18951330.16552449X-RAY DIFFRACTION100
3.5-39.90.20621350.1832590X-RAY DIFFRACTION99.96

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