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

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Basic information

Entry
Database: PDB / ID: 6rzo
TitleCrystal structure of the N-terminal carbohydrate binding module family 48 and ferulic acid esterase from the multi-enzyme CE1-GH62-GH10
Components(Ferulic acid esterase) x 2
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: 1.632 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
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.title
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)77,8582
Polymers77,8582
Non-polymers00
Water15,781876
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-20 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.595, 99.816, 114.429
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: 38872.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: feruloyl esterase
#2: Protein Ferulic acid esterase


Mass: 38985.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: feruloyl esterase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0 w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS propane pH 6.5, 200 mM sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.632→49.638 Å / Num. obs: 90065 / % possible obs: 94.38 % / Redundancy: 6.7 % / Net I/σ(I): 7.09
Reflection shellResolution: 1.632→1.69 Å

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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: 1.632→49.638 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 19.31
RfactorNum. reflection% reflection
Rfree0.1948 4438 4.93 %
Rwork0.1701 --
obs0.1713 89975 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.632→49.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 0 876 6324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095634
X-RAY DIFFRACTIONf_angle_d0.8647646
X-RAY DIFFRACTIONf_dihedral_angle_d12.9043324
X-RAY DIFFRACTIONf_chiral_restr0.062788
X-RAY DIFFRACTIONf_plane_restr0.0061021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6321-1.65070.352920.29831847X-RAY DIFFRACTION62
1.6507-1.67010.31711060.29282081X-RAY DIFFRACTION69
1.6701-1.69050.30411070.27442190X-RAY DIFFRACTION73
1.6905-1.71190.32071180.26822307X-RAY DIFFRACTION77
1.7119-1.73440.27941410.27072403X-RAY DIFFRACTION82
1.7344-1.75820.281390.25032581X-RAY DIFFRACTION86
1.7582-1.78330.26641390.24682683X-RAY DIFFRACTION90
1.7833-1.80990.29131430.23932818X-RAY DIFFRACTION94
1.8099-1.83820.25421500.22432971X-RAY DIFFRACTION99
1.8382-1.86830.28361520.2082985X-RAY DIFFRACTION100
1.8683-1.90050.23521500.20213013X-RAY DIFFRACTION100
1.9005-1.93510.22741390.1942993X-RAY DIFFRACTION100
1.9351-1.97230.21441640.18912991X-RAY DIFFRACTION100
1.9723-2.01260.20631500.18022993X-RAY DIFFRACTION100
2.0126-2.05630.19641650.17132963X-RAY DIFFRACTION99
2.0563-2.10420.2261660.16753011X-RAY DIFFRACTION100
2.1042-2.15680.20081550.16812975X-RAY DIFFRACTION100
2.1568-2.21510.20031590.15713023X-RAY DIFFRACTION100
2.2151-2.28030.19411510.16293003X-RAY DIFFRACTION100
2.2803-2.35390.19891800.15262982X-RAY DIFFRACTION100
2.3539-2.4380.19611540.15843047X-RAY DIFFRACTION100
2.438-2.53560.18461470.15923018X-RAY DIFFRACTION100
2.5356-2.6510.20521700.16123012X-RAY DIFFRACTION100
2.651-2.79080.18211810.16213024X-RAY DIFFRACTION100
2.7908-2.96560.16881450.16693026X-RAY DIFFRACTION100
2.9656-3.19460.18391470.16243060X-RAY DIFFRACTION100
3.1946-3.5160.18381520.15163065X-RAY DIFFRACTION100
3.516-4.02450.14261510.14263091X-RAY DIFFRACTION100
4.0245-5.06970.13941650.12953122X-RAY DIFFRACTION100
5.0697-49.66110.18811600.17663259X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 58.2578 Å / Origin y: 43.5699 Å / Origin z: 38.9441 Å
111213212223313233
T0.1063 Å2-0.0001 Å2-0.0033 Å2-0.0828 Å20.0005 Å2--0.128 Å2
L0.5429 °2-0.0955 °2-0.2344 °2-0.3602 °20.0499 °2--1.1576 °2
S-0.0059 Å °0.0446 Å °-0.0104 Å °0.0034 Å °-0.0368 Å °0.0304 Å °-0.0514 Å °-0.0698 Å °0.0351 Å °
Refinement TLS groupSelection details: all

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