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- PDB-5cxu: Structure of the CE1 ferulic acid esterase AmCE1/Fae1A, from the ... -

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Basic information

Entry
Database: PDB / ID: 5cxu
TitleStructure of the CE1 ferulic acid esterase AmCE1/Fae1A, from the anaerobic fungi Anaeromyces mucronatus in the absence of substrate
Componentsferulic acid esterase AmCE1/Fae1A
KeywordsHYDROLASE / Ferulic acid / esterase / induced fit / alpha/beta hydrolase
Function / homology
Function and homology information


feruloyl esterase / feruloyl esterase activity
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnaeromyces mucronatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGruninger, R.J. / Abbott, D.W.
CitationJournal: Biochem.J. / Year: 2016
Title: Contributions of a unique beta-clamp to substrate recognition illuminates the molecular basis of exolysis in ferulic acid esterases.
Authors: Gruninger, R.J. / Cote, C. / McAllister, T.A. / Abbott, D.W.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ferulic acid esterase AmCE1/Fae1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1712
Polymers31,0791
Non-polymers921
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.870, 101.870, 52.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein ferulic acid esterase AmCE1/Fae1A


Mass: 31078.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaeromyces mucronatus (fungus) / Gene: fae1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2YCB6, feruloyl esterase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Ammonium acetate, 100 mM Sodium acetate (pH 4.6), 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→46.6 Å / Num. obs: 35462 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 5 % / Biso Wilson estimate: 20.46 Å2 / Rmerge(I) obs: 0.0407 / Rsym value: 0.0455 / Net I/av σ(I): 21.9 / Net I/σ(I): 21.9
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5089 / Mean I/σ(I) obs: 2.48 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JT2

1jt2


Resolution: 1.6→46.6 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1649 1774 5 %Random Selection
Rwork0.1396 ---
obs0.1408 35462 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 6 215 2354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142232
X-RAY DIFFRACTIONf_angle_d1.4063037
X-RAY DIFFRACTIONf_dihedral_angle_d13.487831
X-RAY DIFFRACTIONf_chiral_restr0.079327
X-RAY DIFFRACTIONf_plane_restr0.008396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64330.23431360.2172579X-RAY DIFFRACTION100
1.6433-1.69160.22221350.19342570X-RAY DIFFRACTION100
1.6916-1.74620.1971360.17762579X-RAY DIFFRACTION100
1.7462-1.80870.18671370.15492598X-RAY DIFFRACTION100
1.8087-1.88110.17131350.15042572X-RAY DIFFRACTION100
1.8811-1.96670.15761370.13922591X-RAY DIFFRACTION100
1.9667-2.07040.16021360.13442590X-RAY DIFFRACTION100
2.0704-2.20010.1951370.13372594X-RAY DIFFRACTION100
2.2001-2.36990.15551350.13782579X-RAY DIFFRACTION100
2.3699-2.60840.16051370.14172604X-RAY DIFFRACTION100
2.6084-2.98580.16941370.14332589X-RAY DIFFRACTION99
2.9858-3.76160.16011360.1282598X-RAY DIFFRACTION99
3.7616-46.67290.14651400.132645X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.89771.1495-0.15432.3545-0.29811.808-0.16530.5438-0.1924-0.51670.2069-0.04260.134-0.1796-0.08890.2905-0.00390.01150.22610.02680.1723-1.871220.0274-64.616
21.83030.4682-0.20681.9245-0.33231.2003-0.08760.26120.0447-0.23440.051-0.1243-0.03260.0880.04560.208-0.00930.05740.17480.03620.17046.240226.2208-60.1433
34.413-2.42361.01723.2389-3.95927.5434-0.0567-0.25180.24020.465-0.2066-0.4177-0.21730.28270.24840.2158-0.0491-0.00060.1780.00430.197913.104429.6687-46.8024
42.7962-0.10580.49210.2148-0.35520.754-0.09370.20530.3675-0.1750.10570.0541-0.29020.01420.01940.2947-0.03190.03440.25190.09880.31057.155138.837-63.1798
52.02050.0904-0.27982.3439-0.18662.23160.0263-0.06430.1815-0.03280.00390.0233-0.2123-0.0583-0.03770.18090.00320.03020.16850.00920.18350.681830.1574-48.7953
63.7282-1.27850.47244.81220.90925.2845-0.0848-0.57430.32660.55850.2101-0.56250.160.378-0.10270.25240.01730.01220.3256-0.05930.29241.033530.1045-36.6179
72.587-2.23990.29844.47590.34961.0604-0.1045-0.3081-0.11320.21320.11860.18640.1039-0.0486-0.01060.1650.00170.04470.20410.03270.1778-4.54919.835-41.1921
82.1436-0.1427-0.35141.54660.1272.0752-0.01020.00980.0668-0.10640.08380.1001-0.0871-0.1607-0.07820.1595-0.0120.01190.16780.02650.1835-7.847721.7988-51.7173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 146 )
5X-RAY DIFFRACTION5chain 'A' and (resid 147 through 184 )
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 212 )
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 238 )
8X-RAY DIFFRACTION8chain 'A' and (resid 239 through 274 )

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