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- PDB-7c29: Esterase CrmE10 mutant-D178A -

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Basic information

Entry
Database: PDB / ID: 7c29
TitleEsterase CrmE10 mutant-D178A
ComponentsCarboxylesterase
KeywordsHYDROLASE / Esterase CrmE10 mutant-D178A
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / phosphatidylcholine lysophospholipase activity / metal ion binding / ACETATE ION / Carboxylesterase
Function and homology information
Biological speciesCroceicoccus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 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 7, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 20, 2020ID: 6M42
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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_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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_asym_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: Carboxylesterase
B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,06010
Polymers44,6582
Non-polymers4038
Water6,431357
1
A: Carboxylesterase
hetero molecules

A: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,02210
Polymers44,6582
Non-polymers3658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area7590 Å2
ΔGint-67 kcal/mol
Surface area16570 Å2
MethodPISA
2
B: Carboxylesterase
hetero molecules

B: Carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,09810
Polymers44,6582
Non-polymers4408
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation4_665-x+1,-y+3/2,z+1/21
Buried area7440 Å2
ΔGint-53 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.012, 70.041, 80.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

21B-552-

HOH

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Components

#1: Protein Carboxylesterase / SGNH-hydrolase family esterase / CrmE10


Mass: 22328.912 Da / Num. of mol.: 2 / Mutation: D178A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Croceicoccus marinus (bacteria) / Gene: A9D14_03620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z1F9L9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 250mM Calcium acetate, 100mM imidazole, pH 8.5, 5% PEG 1000, 3% 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 19765 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 17.54 Å2 / Rmerge(I) obs: 0.187 / Net I/σ(I): 12.33
Reflection shellResolution: 2.18→2.22 Å / Rmerge(I) obs: 0.448 / Num. unique obs: 1807

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: 4jgg

4jgg


Resolution: 2.18→47.65 Å / SU ML: 0.2611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0031
RfactorNum. reflection% reflection
Rfree0.2371 987 5 %
Rwork0.1719 --
obs0.1753 19740 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.92 Å2
Refinement stepCycle: LAST / Resolution: 2.18→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 20 357 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912961
X-RAY DIFFRACTIONf_angle_d1.00314014
X-RAY DIFFRACTIONf_chiral_restr0.0683449
X-RAY DIFFRACTIONf_plane_restr0.0055552
X-RAY DIFFRACTIONf_dihedral_angle_d16.74711104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.290.29481170.20822621X-RAY DIFFRACTION99.89
2.29-2.440.29641430.17472648X-RAY DIFFRACTION99.89
2.44-2.630.27241440.18332638X-RAY DIFFRACTION99.86
2.63-2.890.27751340.18032679X-RAY DIFFRACTION99.79
2.89-3.310.25811300.18122656X-RAY DIFFRACTION99.71
3.31-4.170.19261550.14622701X-RAY DIFFRACTION99.69
4.17-47.650.20151640.16672810X-RAY DIFFRACTION99.53

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