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- PDB-7c4d: Marine microorganism esterase -

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Basic information

Entry
Database: PDB / ID: 7c4d
TitleMarine microorganism esterase
ComponentsPutative esterase
KeywordsHYDROLASE
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / ACETATE ION / Putative esterase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsZhu, C.H. / Wu, Y.K. / Isupov, M.N.
CitationJournal: J.Agric.Food Chem. / Year: 2021
Title: Structural Insights into a Novel Esterase from the East Pacific Rise and Its Improved Thermostability by a Semirational Design.
Authors: Zhu, C. / Chen, Y. / Isupov, M.N. / Littlechild, J.A. / Sun, L. / Liu, X. / Wang, Q. / Gong, H. / Dong, P. / Zhang, N. / Wu, Y.
History
DepositionMay 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9255
Polymers30,6461
Non-polymers2794
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-21 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.000, 67.000, 62.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Putative esterase / Carboxylesterases


Mass: 30646.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S1GUX0
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 8000, 50mM Li2SO4, 50mM Na2SO4, MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.03→58.024 Å / Num. obs: 20051 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 60.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.5
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 4.3 % / Rmerge(I) obs: 2.13 / Num. unique obs: 1421 / CC1/2: 0.354 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
Cootmodel building
DMMultimodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bf8

3bf8


Resolution: 2.03→58.02 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.692 / SU ML: 0.169 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.184
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2613 1052 5.256 %
Rwork0.1999 18963 -
all0.203 --
obs-20015 99.597 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 68.586 Å2
Baniso -1Baniso -2Baniso -3
1--0.547 Å2-0.273 Å20 Å2
2---0.547 Å2-0 Å2
3---1.773 Å2
Refinement stepCycle: LAST / Resolution: 2.03→58.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 17 66 2171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122187
X-RAY DIFFRACTIONr_angle_refined_deg1.431.6312958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27123.491106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41315405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.927159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021638
X-RAY DIFFRACTIONr_nbd_refined0.1980.2954
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21454
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.270
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.210
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2490.23
X-RAY DIFFRACTIONr_mcbond_it5.3586.5841055
X-RAY DIFFRACTIONr_mcangle_it7.3879.8521319
X-RAY DIFFRACTIONr_scbond_it6.5427.0441132
X-RAY DIFFRACTIONr_scangle_it9.29510.3351636
X-RAY DIFFRACTIONr_lrange_it13.206125.0629116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.03-2.0830.3611010.39813150.39514780.6560.64595.80510.4
2.083-2.140.377780.34113560.34314350.7160.69899.93030.343
2.14-2.2020.414880.33413190.33914070.6970.7531000.331
2.202-2.2690.38750.37212900.37213780.760.77599.05660.368
2.269-2.3440.322540.27912720.28113260.8570.8731000.255
2.344-2.4260.231460.25912290.25812760.9080.89599.92160.236
2.426-2.5170.314620.2511790.25412420.8650.90199.91950.227
2.517-2.620.308530.25211280.25511810.9110.9121000.232
2.62-2.7360.234590.23710800.23711390.9210.9191000.222
2.736-2.8690.302700.22810320.23311020.9070.9281000.218
2.869-3.0240.305560.2159780.2210340.8990.9411000.216
3.024-3.2070.243520.2199450.229980.9290.93999.89980.227
3.207-3.4270.241460.2028830.2049290.9450.9511000.215
3.427-3.7010.196440.1888040.1898480.9580.9621000.205
3.701-4.0530.248380.1727400.1757780.9440.9651000.192
4.053-4.5280.221420.1596880.1627300.9430.9671000.183
4.528-5.2230.189280.1526070.1546350.9680.9691000.182
5.223-6.3840.251180.1595150.1625330.9360.9651000.184
6.384-8.9750.224300.1833860.1864160.9360.951000.21
8.975-58.0240.41120.1662170.1792310.8190.90199.13420.207

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