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- PDB-7xrv: Bacteroides thetaiotaomicron ferulic acid esterase - S150A (BT_40... -

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Basic information

Entry
Database: PDB / ID: 7xrv
TitleBacteroides thetaiotaomicron ferulic acid esterase - S150A (BT_4077-S150A) complex with trans-methylferulate
ComponentsFerulic acid esterase
KeywordsHYDROLASE / Esterase / Complex
Function / homology: / Esterase-like / Putative esterase / acyltransferase activity, transferring groups other than amino-acyl groups / Alpha/Beta hydrolase fold / metal ion binding / Trans-methylferulate / Endo-1,4-beta-xylanase Z
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.713 Å
AuthorsDu, G.M. / Wang, Y.L. / Xin, F.J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Distinct Adjacent Substrate Binding Pocket Regulates the Activity of a Decameric Feruloyl Esterase from Bacteroides thetaiotaomicron.
Authors: Wang, Y. / Du, G. / Zhang, Y. / Yu, H. / Liu, S. / Wang, Z. / Ma, X. / Wei, X. / Wen, B. / Li, Z. / Fan, S. / 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_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)335,09727
Polymers333,23810
Non-polymers1,85817
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20630 Å2
ΔGint-159 kcal/mol
Surface area98540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.854, 153.548, 165.548
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: 33323.828 Da / Num. of mol.: 10 / Mutation: S150A
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-SZQ / Trans-methylferulate / methyl (~{E})-3-(3-methoxy-4-oxidanyl-phenyl)prop-2-enoate


Mass: 208.211 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C11H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.16 M succinic acid (pH 7.0), 16% (w/v) PEG3350, 0.2 M sodium iodide, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.71→109.86 Å / Num. obs: 101667 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.958 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.08 / Rrim(I) all: 0.241 / Net I/σ(I): 10.8 / Num. measured all: 969467 / Scaling rejects: 4427
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.71-2.868.21.068120484147010.760.3921.1382.9100
8.58-109.8610.60.0793702634800.9970.0250.08321.599.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XRT

7xrt


Resolution: 2.713→109.859 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1987 1.97 %
Rwork0.1792 99120 -
obs0.1801 101107 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.44 Å2 / Biso mean: 43.7279 Å2 / Biso min: 8.7 Å2
Refinement stepCycle: final / Resolution: 2.713→109.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21551 0 105 462 22118
Biso mean--71.5 35.9 -
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 (%)
2.7131-2.7810.2981420.23437019100
2.781-2.85610.29391380.22387051100
2.8561-2.94020.30491450.22817037100
2.9402-3.03510.29881440.2347071100
3.0351-3.14360.28921350.21167035100
3.1436-3.26950.22861470.19197069100
3.2695-3.41830.2941340.2077103100
3.4183-3.59850.29151420.2275699599
3.5985-3.8240.27281420.2223696298
3.824-4.11920.26281400.198690497
4.1192-4.53380.15411440.12867133100
4.5338-5.18980.16031440.11697177100
5.1898-6.53850.19191450.14997221100
6.5385-109.8590.1641450.1387734398

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