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- PDB-7xrt: Bacteroides thetaiotaomicron ferulic acid esterase (BT_4077) -

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Basic information

Entry
Database: PDB / ID: 7xrt
TitleBacteroides thetaiotaomicron ferulic acid esterase (BT_4077)
ComponentsFerulic acid esterase
KeywordsHYDROLASE / esterase
Function / homology: / Esterase-like / Putative esterase / acyltransferase activity, transferring groups other than amino-acyl groups / Alpha/Beta hydrolase fold / metal ion binding / Endo-1,4-beta-xylanase Z
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsDu, G.M. / Wang, Y.L. / Xin, F.J.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural insights into the oligomeric effects on catalytic activity of a decameric feruloyl esterase and its application in ferulic acid production.
Authors: Du, G. / Wang, Y. / Zhang, Y. / Yu, H. / Liu, S. / Ma, X. / Cao, H. / Wei, X. / Wen, B. / Li, Z. / Fan, S. / Zhou, H. / Xin, F.
History
DepositionMay 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_related / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferulic acid esterase
B: Ferulic acid esterase
C: Ferulic acid esterase
D: Ferulic acid esterase
E: Ferulic acid esterase
F: Ferulic acid esterase
G: Ferulic acid esterase
H: Ferulic acid esterase
I: Ferulic acid esterase
J: Ferulic acid esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,86329
Polymers333,39810
Non-polymers1,46419
Water33,8861881
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23210 Å2
ΔGint-244 kcal/mol
Surface area96160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.385, 160.164, 192.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ferulic acid esterase


Mass: 33339.828 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50
Gene: BT_4077 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A0E4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1881 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.04 M Sodium cacodylate trihydrate (pH 6.0), 60% (v/v) MPD, 0.04 M potassium chloride, 0.012 M Spermine tetrahydrochloride, 0.02 M Trimethylamine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 229659 / % possible obs: 98.9 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Χ2: 0.78 / Net I/σ(I): 10.3 / Num. measured all: 2788140
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0711.40.675225210.9260.1980.7040.56898.1
2.07-2.1511.70.446226790.970.130.4650.51298.4
2.15-2.2511.50.337226950.9790.10.3520.60798.6
2.25-2.3711.60.232226950.9880.0690.2430.60498.6
2.37-2.5212.40.177228120.9940.0510.1850.64698.9
2.52-2.7112.30.132229460.9970.0390.1380.79799.1
2.71-2.99130.09230020.9980.0260.0940.99499.3
2.99-3.4213.10.064231780.9990.0180.0661.08599.4
3.42-4.3113.20.048232710.9990.0140.050.93599.6
4.31-5011.10.038238600.9990.0120.040.9599.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VOL

5vol


Resolution: 2.007→29.351 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1715 11285 4.92 %
Rwork0.152 218216 -
obs0.153 229501 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.47 Å2 / Biso mean: 40.0273 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 2.007→29.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21495 0 82 1881 23458
Biso mean--67.29 42.03 -
Num. residues----2680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.007-2.02940.22913370.1892634987
2.0294-2.05330.22183570.1928718898
2.0533-2.07830.21943330.1968722398
2.0783-2.10460.2223870.1838717598
2.1046-2.13230.21793800.1763720498
2.1323-2.16150.19853690.1704718498
2.1615-2.19240.19113870.1711718798
2.1924-2.22510.21563970.1707721899
2.2251-2.25980.21253280.1725725699
2.2598-2.29690.18543470.168723599
2.2969-2.33650.20393600.1638722299
2.3365-2.37890.21283780.1706723299
2.3789-2.42470.20163720.1655729499
2.4247-2.47410.18943890.1618724499
2.4741-2.52790.17024070.1638722799
2.5279-2.58670.19783990.161724799
2.5867-2.65130.18723840.1661729499
2.6513-2.72290.19283800.171728999
2.7229-2.8030.19353710.1608731899
2.803-2.89340.18313580.1642735199
2.8934-2.99670.17683710.1606729699
2.9967-3.11660.18893790.1592735599
3.1166-3.25820.17023880.14967348100
3.2582-3.42980.17433770.1505737899
3.4298-3.64430.15523680.1395739399
3.6443-3.92510.1454150.13237397100
3.9251-4.3190.12344060.12387382100
4.319-4.94140.13193830.1197491100
4.9414-6.21580.17854040.15057533100
6.2158-29.3510.15523740.1557770698

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