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- PDB-7c2a: Crystal structure of AlinE4, a SGNH-hydrolase family esterase -

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Basic information

Entry
Database: PDB / ID: 7c2a
TitleCrystal structure of AlinE4, a SGNH-hydrolase family esterase
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
Function and homology information
Biological speciesAltererythrobacter indicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.18 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: 6M43
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)21,2818
Polymers20,7081
Non-polymers5737
Water3,981221
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)79.783, 79.783, 61.010
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-316-

HOH

21A-501-

HOH

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Components

#1: Protein SGNH-hydrolase family esterase / AlinE4


Mass: 20707.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Altererythrobacter indicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYH5
#2: Chemical ChemComp-CD / CADMIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 47.35 %
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: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.18→48.46 Å / Num. obs: 64618 / % possible obs: 99.03 % / Redundancy: 2 % / Biso Wilson estimate: 11.53 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 20
Reflection shellResolution: 1.18→1.21 Å / Rmerge(I) obs: 0.645 / Num. unique obs: 4370

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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: 1.18→48.46 Å / SU ML: 0.0774 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.5187
RfactorNum. reflection% reflection
Rfree0.1827 1999 3.09 %
Rwork0.1763 --
obs0.1765 64602 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.89 Å2
Refinement stepCycle: LAST / Resolution: 1.18→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 24 221 1684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921596
X-RAY DIFFRACTIONf_angle_d1.06362166
X-RAY DIFFRACTIONf_chiral_restr0.093236
X-RAY DIFFRACTIONf_plane_restr0.0077295
X-RAY DIFFRACTIONf_dihedral_angle_d19.0418613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.210.24381300.23534063X-RAY DIFFRACTION91.43
1.21-1.240.23251400.22354375X-RAY DIFFRACTION98.17
1.24-1.280.17981400.21194384X-RAY DIFFRACTION99.12
1.28-1.320.23251410.20454443X-RAY DIFFRACTION99.54
1.32-1.370.20261420.20054434X-RAY DIFFRACTION99.33
1.37-1.420.18451420.18964446X-RAY DIFFRACTION99.57
1.42-1.490.16241430.18444480X-RAY DIFFRACTION99.83
1.49-1.560.1741440.17414485X-RAY DIFFRACTION99.78
1.56-1.660.20071430.17474480X-RAY DIFFRACTION99.96
1.66-1.790.18591430.17274495X-RAY DIFFRACTION99.98
1.79-1.970.19351460.16594535X-RAY DIFFRACTION100
1.97-2.260.18071440.16664554X-RAY DIFFRACTION99.98
2.26-2.840.17791480.17454598X-RAY DIFFRACTION99.96
2.84-48.460.16791530.16774831X-RAY DIFFRACTION99.98

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