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- PDB-7c84: Esterase AlinE4 mutant, D162A -

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Basic information

Entry
Database: PDB / ID: 7c84
TitleEsterase AlinE4 mutant, D162A
ComponentsSGNH-hydrolase family esterase
KeywordsHYDROLASE / esterase / SGNH-hydrolase family / marine
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / lysophospholipase activity / SGNH hydrolase superfamily / ACETATE ION / : / SGNH-hydrolase family esterase / SGNH-hydrolase family esterase
Function and homology information
Biological speciesAltererythrobacter indicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 Å
AuthorsLi, Z. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: Biotechnol Biofuels / Year: 2020
Title: Structure-guided protein engineering increases enzymatic activities of the SGNH family esterases.
Authors: Li, Z. / Li, L. / Huo, Y. / Chen, Z. / Zhao, Y. / Huang, J. / Jian, S. / Rong, Z. / Wu, D. / Gan, J. / Hu, X. / Li, J. / Xu, X.W.
History
DepositionMay 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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

Downloads & links

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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
Buried area710 Å2
ΔGint-19 kcal/mol
Surface area12360 Å2
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
Components on special symmetry positions
IDModelComponents
11A-472-

HOH

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Components

#1: Protein SGNH-hydrolase family esterase


Mass: 20663.711 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, 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 / pH: 7.5
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: 1.552→48.42 Å / Num. obs: 29037 / % possible obs: 99.97 % / Redundancy: 2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 32.71
Reflection shellResolution: 1.552→1.607 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 2859

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JGG

4jgg


Resolution: 1.552→48.42 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.827 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1538 1496 5.152 %
Rwork0.1144 27542 -
all0.116 --
obs-27541 99.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.066 Å20 Å20 Å2
2--0.066 Å20 Å2
3----0.132 Å2
Refinement stepCycle: LAST / Resolution: 1.552→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 18 188 1642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131562
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171510
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.6432119
X-RAY DIFFRACTIONr_angle_other_deg1.6251.5793508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7835206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6221.39279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5215272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9241513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021803
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02324
X-RAY DIFFRACTIONr_nbd_refined0.2430.2347
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21383
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2792
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1190.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3250.223
X-RAY DIFFRACTIONr_nbd_other0.260.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.219
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1840.22
X-RAY DIFFRACTIONr_mcbond_it1.851.228802
X-RAY DIFFRACTIONr_mcbond_other1.7561.22799
X-RAY DIFFRACTIONr_mcangle_it2.2851.8411014
X-RAY DIFFRACTIONr_mcangle_other2.2931.8441015
X-RAY DIFFRACTIONr_scbond_it3.8311.67760
X-RAY DIFFRACTIONr_scbond_other3.8291.67761
X-RAY DIFFRACTIONr_scangle_it4.1082.3371105
X-RAY DIFFRACTIONr_scangle_other4.1062.3371106
X-RAY DIFFRACTIONr_lrange_it3.67616.7011817
X-RAY DIFFRACTIONr_lrange_other3.59316.2821784
X-RAY DIFFRACTIONr_rigid_bond_restr3.84833072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.552-1.5920.1231110.0772001X-RAY DIFFRACTION99.9527
1.592-1.6360.1351110.0791946X-RAY DIFFRACTION100
1.636-1.6830.1471140.0781876X-RAY DIFFRACTION100
1.683-1.7350.1421000.0751860X-RAY DIFFRACTION100
1.735-1.7920.145970.0811784X-RAY DIFFRACTION100
1.792-1.8550.156950.0791737X-RAY DIFFRACTION100
1.855-1.9250.107730.091675X-RAY DIFFRACTION100
1.925-2.0030.183770.091637X-RAY DIFFRACTION100
2.003-2.0920.129880.0951553X-RAY DIFFRACTION100
2.092-2.1940.125680.1011486X-RAY DIFFRACTION100
2.194-2.3130.134860.1041412X-RAY DIFFRACTION100
2.313-2.4530.168830.1061352X-RAY DIFFRACTION100
2.453-2.6220.131680.1161267X-RAY DIFFRACTION99.9251
2.622-2.8310.143600.1151188X-RAY DIFFRACTION100
2.831-3.10.147570.1341105X-RAY DIFFRACTION100
3.1-3.4650.138520.1341018X-RAY DIFFRACTION100
3.465-3.9990.175540.145890X-RAY DIFFRACTION99.7886
3.999-4.8910.193430.135763X-RAY DIFFRACTION100
4.891-6.8910.2360.178613X-RAY DIFFRACTION99.8462
6.891-48.420.232230.197379X-RAY DIFFRACTION99.5049

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