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- PDB-9w30: Crystal structure of feruloyl esterase from Clostridium acetobutylicum -

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Basic information

Entry
Database: PDB / ID: 9w30
TitleCrystal structure of feruloyl esterase from Clostridium acetobutylicum
ComponentsAlpha/beta superfamily hydrolase
KeywordsHYDROLASE / feruloyl esterase
Function / homology: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Alpha/beta superfamily hydrolase
Function and homology information
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsXue, S. / Feng, Y. / Li, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2022YFC2105602 China
CitationJournal: To Be Published
Title: Unveiling Enzymatic Plasticity of Feruloyl Esterase from Clostridium acetobutylicum
Authors: Li, S. / Feng, Y. / Xue, S.
History
DepositionJul 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta superfamily hydrolase
B: Alpha/beta superfamily hydrolase
C: Alpha/beta superfamily hydrolase
D: Alpha/beta superfamily hydrolase


Theoretical massNumber of molelcules
Total (without water)116,8944
Polymers116,8944
Non-polymers00
Water2,612145
1
A: Alpha/beta superfamily hydrolase


Theoretical massNumber of molelcules
Total (without water)29,2231
Polymers29,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta superfamily hydrolase


Theoretical massNumber of molelcules
Total (without water)29,2231
Polymers29,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha/beta superfamily hydrolase


Theoretical massNumber of molelcules
Total (without water)29,2231
Polymers29,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha/beta superfamily hydrolase


Theoretical massNumber of molelcules
Total (without water)29,2231
Polymers29,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.260, 69.260, 213.116
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein
Alpha/beta superfamily hydrolase / Feruloyl Esterase


Mass: 29223.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W
Gene: CA_C3665 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q97D17
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Bis Tris, PEG3350, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→48.97 Å / Num. obs: 36468 / % possible obs: 98.76 % / Redundancy: 9.6 % / Biso Wilson estimate: 39.19 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1288 / Rpim(I) all: 0.0447 / Rrim(I) all: 0.1364 / Net I/σ(I): 16.57
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.4107 / Mean I/σ(I) obs: 4.81 / Num. unique obs: 3575 / CC1/2: 0.969 / CC star: 0.992 / Rpim(I) all: 0.1435 / Rrim(I) all: 0.4355 / % possible all: 97.24

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000version 723data reduction
HKL-3000version 723data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48.97 Å / SU ML: 0.2678 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2564 1851 5.13 %
Rwork0.2028 34224 -
obs0.2054 36075 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.73 Å2
Refinement stepCycle: LAST / Resolution: 2.45→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8129 0 0 145 8274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228273
X-RAY DIFFRACTIONf_angle_d0.482711142
X-RAY DIFFRACTIONf_chiral_restr0.03981254
X-RAY DIFFRACTIONf_plane_restr0.00251415
X-RAY DIFFRACTIONf_dihedral_angle_d4.79191095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.520.28641350.26252592X-RAY DIFFRACTION96.91
2.52-2.590.29181320.24452601X-RAY DIFFRACTION98.59
2.59-2.680.29661690.24452601X-RAY DIFFRACTION98.68
2.68-2.770.25921570.23072653X-RAY DIFFRACTION99.08
2.77-2.890.28351310.23212661X-RAY DIFFRACTION99.18
2.89-3.020.29391530.2312597X-RAY DIFFRACTION98.89
3.02-3.180.27011550.23582639X-RAY DIFFRACTION99.18
3.18-3.370.26231530.23332609X-RAY DIFFRACTION99.5
3.37-3.630.28521610.20612657X-RAY DIFFRACTION99.44
3.64-40.28441070.19082662X-RAY DIFFRACTION99.53
4-4.580.18611300.16352691X-RAY DIFFRACTION99.58
4.58-5.760.21251400.17692671X-RAY DIFFRACTION99.5
5.77-48.970.25841280.18152590X-RAY DIFFRACTION96.18

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