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- PDB-6rzn: Crystal structure of the N-terminal carbohydrate binding module f... -

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Basic information

Entry
Database: PDB / ID: 6rzn
TitleCrystal structure of the N-terminal carbohydrate binding module family 48 and ferulic acid esterase from the multi-enzyme CE1-GH62-GH10
ComponentsFerulic acid esterase
KeywordsHYDROLASE / ferulic acid esterease / carbohydrate esterase family 1 / CE1 / CBM48 / carbohydrate binding module family 48
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.907 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF10CC1016517 Denmark
CitationJournal: J.Biol.Chem. / Year: 2019
Title: A carbohydrate-binding family 48 module enables feruloyl esterase action on polymeric arabinoxylan.
Authors: Holck, J. / Fredslund, F. / Moller, M.S. / Brask, J. / Krogh, K.B.R.M. / Lange, L. / Welner, D.H. / Svensson, B. / Meyer, A.S. / Wilkens, C.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferulic acid esterase
B: Ferulic acid esterase


Theoretical massNumber of molelcules
Total (without water)85,5752
Polymers85,5752
Non-polymers00
Water16,970942
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-22 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.650, 99.900, 133.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ferulic acid esterase


Mass: 42787.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The electron density is lacking for the N-terminal and two loops.
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: feruloyl esterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 942 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 50 mM ammonium sulfate, 50 mM Bis-Tris/HCl 6.5,30 % (v/v) pentaerythritol ethoxylate (15/4_EO/OH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.907→54.86 Å / Num. obs: 68057 / % possible obs: 98.49 % / Redundancy: 4.8 % / Net I/σ(I): 6.73
Reflection shellResolution: 1.907→1.975 Å / Num. unique obs: 6769

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JT2

1jt2


Resolution: 1.907→54.86 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 19.52
RfactorNum. reflection% reflection
Rfree0.2046 3488 5.13 %
Rwork0.1756 --
obs0.1771 68019 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.907→54.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 0 942 6308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035500
X-RAY DIFFRACTIONf_angle_d0.6237447
X-RAY DIFFRACTIONf_dihedral_angle_d11.2393225
X-RAY DIFFRACTIONf_chiral_restr0.046788
X-RAY DIFFRACTIONf_plane_restr0.004965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9069-1.9330.24711470.22752571X-RAY DIFFRACTION100
1.933-1.96060.26491380.22512571X-RAY DIFFRACTION100
1.9606-1.98990.25791320.2242599X-RAY DIFFRACTION100
1.9899-2.0210.27331420.21822540X-RAY DIFFRACTION100
2.021-2.05410.25311560.21552567X-RAY DIFFRACTION99
2.0541-2.08950.25331350.19942583X-RAY DIFFRACTION99
2.0895-2.12750.23851280.19082598X-RAY DIFFRACTION99
2.1275-2.16840.21881190.18412559X-RAY DIFFRACTION99
2.1684-2.21270.20741250.18452590X-RAY DIFFRACTION99
2.2127-2.26080.23011360.18012569X-RAY DIFFRACTION98
2.2608-2.31340.20951220.17592517X-RAY DIFFRACTION98
2.3134-2.37130.23191610.17062550X-RAY DIFFRACTION98
2.3713-2.43540.22371390.17622593X-RAY DIFFRACTION98
2.4354-2.5070.22761350.17142557X-RAY DIFFRACTION99
2.507-2.5880.19321370.17252554X-RAY DIFFRACTION99
2.588-2.68040.20961510.16592573X-RAY DIFFRACTION98
2.6804-2.78780.20761360.16772578X-RAY DIFFRACTION98
2.7878-2.91460.19221330.17492569X-RAY DIFFRACTION98
2.9146-3.06830.25541490.17282453X-RAY DIFFRACTION93
3.0683-3.26050.19011190.17862568X-RAY DIFFRACTION97
3.2605-3.51220.20111690.16312604X-RAY DIFFRACTION99
3.5122-3.86560.17741470.15782637X-RAY DIFFRACTION99
3.8656-4.42470.15441350.14932643X-RAY DIFFRACTION99
4.4247-5.57380.15291420.15452685X-RAY DIFFRACTION99
5.5738-54.88640.19751550.19442703X-RAY DIFFRACTION96

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