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- PDB-9jlu: GH57 family amylopullulanase from Aquifex aeolicus D352N mutant c... -

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Basic information

Entry
Database: PDB / ID: 9jlu
TitleGH57 family amylopullulanase from Aquifex aeolicus D352N mutant complex with beta-cyclodextrin
ComponentsGlycoside hydrolase family 57 N-terminal domain-containing protein
KeywordsHYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus
Function / homology: / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / catalytic activity / carbohydrate metabolic process / beta-cyclodextrin / Glycoside hydrolase family 57 N-terminal domain-containing protein
Function and homology information
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZhu, Z.M. / Wang, W.W. / Li, M.J. / Xu, Q. / Zhou, H. / Huang, L.Q. / Wang, Q.S. / Yu, F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J.Struct.Biol. / Year: 2025
Title: Mechanistic insights into cyclodextrins as substrates and inhibitors of GH57 family amylopullulanase from Aquifex aeolicus.
Authors: Zhu, Z. / Li, M. / Xu, Q. / Huang, L. / Zhou, H. / Wang, W. / Wang, Q. / Yu, F.
History
DepositionSep 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8667
Polymers57,2521
Non-polymers1,6136
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.550, 40.610, 63.340
Angle α, β, γ (deg.)90.00, 96.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycoside hydrolase family 57 N-terminal domain-containing protein


Mass: 57252.250 Da / Num. of mol.: 1 / Mutation: D352N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: aq_720 / Production host: Escherichia coli (E. coli) / References: UniProt: O66934
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose)


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 338 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium citrate, pH 4.2, 20% PEG 3350

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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: May 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→33.56 Å / Num. obs: 42138 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 9
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.381 / Num. unique obs: 3111 / CC1/2: 0.474 / Rpim(I) all: 0.562 / Rrim(I) all: 1.493

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→33.558 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 2102 4.99 %
Rwork0.1654 --
obs0.1674 42133 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→33.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 107 226 4385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084281
X-RAY DIFFRACTIONf_angle_d0.8815795
X-RAY DIFFRACTIONf_dihedral_angle_d4.1643585
X-RAY DIFFRACTIONf_chiral_restr0.054621
X-RAY DIFFRACTIONf_plane_restr0.005715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.92380.28281220.2472676X-RAY DIFFRACTION100
1.9238-1.97190.2541440.22112609X-RAY DIFFRACTION100
1.9719-2.02520.24881640.2082644X-RAY DIFFRACTION100
2.0252-2.08480.30011470.19742617X-RAY DIFFRACTION100
2.0848-2.1520.21641670.18822664X-RAY DIFFRACTION100
2.152-2.22890.21421330.17922634X-RAY DIFFRACTION100
2.2289-2.31820.24131330.16712644X-RAY DIFFRACTION100
2.3182-2.42360.22851270.16482696X-RAY DIFFRACTION100
2.4236-2.55140.19421340.16772658X-RAY DIFFRACTION100
2.5514-2.71110.18821530.15482669X-RAY DIFFRACTION100
2.7111-2.92040.18291370.15232662X-RAY DIFFRACTION100
2.9204-3.2140.1871330.15072665X-RAY DIFFRACTION100
3.214-3.67860.19511270.152720X-RAY DIFFRACTION100
3.6786-4.63270.1781430.13892691X-RAY DIFFRACTION100
4.6327-33.5580.21011380.17572782X-RAY DIFFRACTION99
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)
11.2817-0.35730.09740.8493-0.02531.3007-0.01520.0016-0.12340.043-0.00470.05160.06830.0510.0110.1241-0.00910.01420.09990.00350.1225-31.602815.998927.9167
21.8740.07730.97660.98830.22161.9404-0.1079-0.27160.09760.1180.0273-0.0858-0.10440.10520.07510.14720.0364-0.00140.1803-0.0040.1086-21.549621.332443.5282
31.0174-0.4313-0.15890.6920.20651.01240.0390.1739-0.0382-0.1218-0.05510.084-0.0539-0.03440.01450.1389-0.0108-0.01750.1211-0.00450.1338-35.952320.900712.9516
41.4772-0.4975-0.35320.70190.33041.24090.02650.09840.0771-0.0512-0.0058-0.0261-0.03720.1177-0.01250.1515-0.0216-0.00120.08050.01520.1351-26.839320.579416.696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 360 )
4X-RAY DIFFRACTION4chain 'A' and (resid 361 through 477 )

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