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- PDB-9kyp: GH57 family amylopullulanase from Aquifex aeolicus wild type comp... -

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Basic information

Entry
Database: PDB / ID: 9kyp
TitleGH57 family amylopullulanase from Aquifex aeolicus wild type complex with beta-cyclodextrin
Components(Glycoside hydrolase family 57 N-terminal domain-containing ...) x 2
KeywordsHYDROLASE / GH57 family / amylopullulanase / Aquifex aeolicus
Function / homology
Function and homology information


catalytic activity / carbohydrate metabolic process
Similarity search - Function
: / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
beta-cyclodextrin / DI(HYDROXYETHYL)ETHER / Glycoside hydrolase family 57 N-terminal domain-containing protein
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsZhu, Z.M. / Wang, W.W. / Yu, F. / Li, M.J. / Xu, Q. / Zhou, H. / Huang, L.Q. / Wang, Q.S.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
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
DepositionDec 9, 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
B: Glycoside hydrolase family 57 N-terminal domain-containing protein
C: Glycoside hydrolase family 57 N-terminal domain-containing protein
D: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,54433
Polymers231,8724
Non-polymers6,67229
Water19,0421057
1
A: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,00610
Polymers58,2061
Non-polymers1,8009
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6986
Polymers58,2061
Non-polymers1,4915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6686
Polymers58,2061
Non-polymers1,4615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 57 N-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,17311
Polymers57,2531
Non-polymers1,92010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.830, 61.500, 195.540
Angle α, β, γ (deg.)84.04, 89.46, 89.09
Int Tables number1
Space group name H-MP1

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Components

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Glycoside hydrolase family 57 N-terminal domain-containing ... , 2 types, 4 molecules ABCD

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


Mass: 58206.355 Da / Num. of mol.: 3
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: Protein Glycoside hydrolase family 57 N-terminal domain-containing protein / GH57 family amylopullulanase


Mass: 57253.234 Da / Num. of mol.: 1
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

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Sugars , 1 types, 4 molecules

#3: Polysaccharide
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 4
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

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Non-polymers , 4 types, 1082 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.31 %
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: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.79→64.83 Å / Num. obs: 169216 / % possible obs: 94.9 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.086 / Rrim(I) all: 0.161 / Χ2: 0.84 / Net I/σ(I): 7.5 / Num. measured all: 584041
Reflection shellResolution: 1.79→1.84 Å / % possible obs: 94.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.954 / Num. measured all: 41650 / Num. unique obs: 12393 / CC1/2: 0.512 / Rpim(I) all: 0.607 / Rrim(I) all: 1.134 / Χ2: 0.73 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→24.32 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 8300 4.91 %
Rwork0.154 --
obs0.1557 169138 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16088 0 442 1057 17587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117075
X-RAY DIFFRACTIONf_angle_d1.03823130
X-RAY DIFFRACTIONf_dihedral_angle_d5.47314172
X-RAY DIFFRACTIONf_chiral_restr0.0622487
X-RAY DIFFRACTIONf_plane_restr0.0072859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.81030.3163100.24785294X-RAY DIFFRACTION94
1.8103-1.83160.28062620.2325285X-RAY DIFFRACTION94
1.8316-1.8540.25632800.21235403X-RAY DIFFRACTION95
1.854-1.87740.23722710.20375330X-RAY DIFFRACTION95
1.8774-1.90210.24022890.20255250X-RAY DIFFRACTION95
1.9021-1.92820.25482830.19695479X-RAY DIFFRACTION95
1.9282-1.95570.21652820.18595390X-RAY DIFFRACTION95
1.9557-1.98490.23682890.18085359X-RAY DIFFRACTION95
1.9849-2.01590.22312630.17295370X-RAY DIFFRACTION95
2.0159-2.04890.21432830.16685458X-RAY DIFFRACTION96
2.0489-2.08420.22652960.1615263X-RAY DIFFRACTION95
2.0842-2.12210.18863440.15885382X-RAY DIFFRACTION95
2.1221-2.16290.18892910.15665375X-RAY DIFFRACTION96
2.1629-2.2070.19152380.15185440X-RAY DIFFRACTION96
2.207-2.2550.2092430.15765479X-RAY DIFFRACTION96
2.255-2.30740.20422560.15565417X-RAY DIFFRACTION96
2.3074-2.3650.19972930.15685442X-RAY DIFFRACTION96
2.365-2.42890.20342350.16215415X-RAY DIFFRACTION96
2.4289-2.50030.20142920.15755381X-RAY DIFFRACTION96
2.5003-2.58090.20012820.15745423X-RAY DIFFRACTION95
2.5809-2.67310.1962810.15255401X-RAY DIFFRACTION95
2.6731-2.780.19063120.15475281X-RAY DIFFRACTION95
2.78-2.90630.20432830.1545351X-RAY DIFFRACTION94
2.9063-3.05920.19282570.15415315X-RAY DIFFRACTION94
3.0592-3.25050.19492580.15135345X-RAY DIFFRACTION94
3.2505-3.50080.16772490.14425277X-RAY DIFFRACTION93
3.5008-3.85180.16222710.13165241X-RAY DIFFRACTION93
3.8518-4.40640.13292860.12285263X-RAY DIFFRACTION93
4.4064-5.54070.15292530.13195370X-RAY DIFFRACTION95
5.5407-24.320.17332680.15515359X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.40350.06020.1261.01650.41881.04320.0026-0.02-0.03240.01820.00290.12060.0523-0.0483-0.0020.0892-0.0110.00620.1366-0.00030.1605-22.1907-31.978730.0903
20.4527-0.7313-0.75591.63041.36252.01650.02160.0398-0.1335-0.3275-0.11720.35720.0676-0.19110.06440.2014-0.0155-0.03870.17480.00090.1917-27.3418-39.141414.364
30.84220.29250.19091.58020.92881.8022-0.06030.1361-0.0191-0.34650.0484-0.32890.00950.3336-0.02150.21180.01350.05810.2386-0.00590.217-9.0882-43.59211.5555
40.4904-0.3435-0.32451.60350.91541.79870.01280.0282-0.0970.00430.00380.04060.2445-0.0501-0.00820.1627-0.0132-0.01050.13750.00840.2099-21.2588-47.709623.5616
50.25150.08410.03751.2253-0.18240.9469-0.0216-0.01110.0306-0.0182-0.01620.0923-0.0855-0.07130.02280.09540.00810.0050.1583-0.0110.183-26.4702-13.427430.0562
60.9272-0.53010.05521.33760.18980.8467-0.02010.0560.06240.08540.0106-0.0802-0.08410.0779-0.00510.0993-0.01850.0050.1601-0.00210.1789-11.6027-16.856240.336
70.98030.19720.2091.63970.82362.14460.0444-0.0972-0.05560.25960.0013-0.10180.11740.0338-0.03590.1355-0.0048-0.00350.14920.02230.1578-11.7898-29.846344.4539
80.8457-0.0459-0.16121.16820.0241.9303-0.03940.03730.0775-0.1364-0.0155-0.0846-0.13810.21170.05870.1568-0.01490.00050.13630.02180.2024-17.7272-9.479522.0442
91.512-0.30620.242.97990.06282.48030.04530.065-0.0515-0.3413-0.03380.04720.03350.04380.00440.1983-0.0074-0.02180.1490.00810.1593-23.7315-19.723312.2684
100.7157-0.191-0.00031.0920.26410.4729-0.0091-0.00060.0251-0.0073-0.03690.0916-0.0361-0.03650.03920.16830.016-0.01020.1376-0.00490.1551-28.321-31.7028-25.0801
110.48760.4899-0.06580.70560.41.04280.0683-0.08560.08150.189-0.0589-0.0298-0.0972-0.0401-0.00820.27390.0022-0.00990.18910.00480.1704-21.4307-22.1079-5.7344
120.63590.19070.05642.13541.37692.1881-0.0170.04520.1227-0.090.1117-0.2564-0.19610.3044-0.06820.2358-0.01510.00850.1915-0.00950.2335-14.3527-14.8829-16.3036
131.08191.05571.2562.5732.16832.4075-0.0548-0.0690.1158-0.159-0.14270.2732-0.2071-0.18490.21850.21140.04720.00210.17390.01660.214-32.1963-19.5043-22.8153
140.5946-0.24830.1331.6311-0.35171.29280.0679-0.0455-0.0994-0.0183-0.00770.18120.1686-0.1119-0.0550.1878-0.0091-0.00780.184-0.00910.1958-31.4276-50.3639-22.1365
151.1226-0.551-0.21140.9030.45040.73070.0780.1135-0.0452-0.0828-0.06490.20720.0882-0.1563-0.00310.2185-0.0125-0.04560.2023-0.00290.226-32.8199-49.6201-31.3682
161.26630.8937-0.11761.2825-0.0050.7643-0.12580.0134-0.0561-0.19920.0604-0.05660.06250.06250.02970.19530.0383-0.01040.1849-0.01310.1709-19.3391-47.3014-38.5237
170.83220.0195-0.01051.38570.37611.37520.04610.16010.0249-0.1619-0.0148-0.04280.0470.0383-0.03020.23470.0341-0.0010.2090.00580.1576-19.5947-34.1135-42.3931
180.987-0.04130.14611.2055-0.24061.6888-0.0064-0.0307-0.02550.16260.0064-0.07870.19310.18770.00880.22310.0114-0.01830.140.00490.2089-21.9896-54.2792-19.2025
191.28440.36650.1913.2486-0.03651.97070.0299-0.0724-0.05490.3628-0.0436-0.06320.01730.08080.00150.20370.0208-0.0120.14330.00470.1268-25.8982-43.9916-8.5838
200.72160.0371-0.02151.68790.75671.1011-0.04060.0264-0.0513-0.15660.06150.15440.0118-0.0645-0.01170.1628-0.0199-0.00520.17320.00580.1807-8.7536-15.7481-68.5422
210.7753-0.4903-0.39070.81270.31521.44250.08060.0912-0.0644-0.3844-0.04550.1595-0.0052-0.02820.00420.4183-0.0045-0.01860.2577-0.00190.2273-3.0494-22.3347-89.644
220.629-0.3655-0.69481.28361.46582.0769-0.06770.0321-0.1357-0.43810.1638-0.54230.23750.6769-0.04680.32060.01190.06740.3206-0.0390.261510.202-28.5555-83.0508
230.6281-0.2473-0.39381.52040.22991.4809-0.0173-0.0106-0.1242-0.12330.02160.12130.279-0.05350.0260.2586-0.0429-0.02310.1954-0.00390.22-6.1462-30.726-76.4407
240.7847-0.2473-0.02131.86270.69181.88490.00030.03630.0967-0.19910.03880.1797-0.2938-0.0385-0.04540.22170.004-0.01570.20090.01040.2171-11.51142.4265-64.9437
250.72610.0024-0.2971.26950.1551.16-0.0415-0.11170.05770.1250.095-0.1528-0.03290.2493-0.04840.1859-0.0106-0.02030.2686-0.02250.21213.0699-8.1728-53.106
260.6930.28890.0951.5570.54232.3335-0.0982-0.173-0.05710.36930.07760.04180.21360.04430.01130.19620.0096-0.00640.18310.02610.1941-3.1491-18.0253-50.3162
271.2841-0.1061-0.38551.6965-0.24742.34170.08760.09420.128-0.51280.1261-0.1375-0.39280.3224-0.14020.3677-0.05040.04980.15240.01570.2227-1.57857.3018-71.0678
281.1911-0.1559-0.18583.29050.39882.68360.02650.28860.0614-0.67510.01980.0039-0.3853-0.0101-0.07190.4563-0.0493-0.01520.23310.0270.1815-6.5467-1.1176-82.9675
290.6818-0.1231-0.16941.15510.32060.6706-0.0179-0.03850.02560.1430.0190.0465-0.0024-0.094-0.00590.11590.0140.01110.1603-0.00790.1513-4.3198-47.699371.3275
300.67320.30270.32891.9120.6152.25960.0475-0.11440.06650.42730.0171-0.0817-0.20640.0415-0.06910.26110.00860.00570.1772-0.0150.1920.6523-35.634985.347
310.9011-0.1968-0.01591.44340.20051.4625-0.0113-0.0064-0.07420.09140.01270.10020.1818-0.0886-0.01090.1275-0.01750.01510.17330.00550.1696-7.1415-65.773867.7812
321.43040.77430.04461.7567-0.09980.7107-0.049-0.1149-0.0987-0.1728-0.0414-0.23570.04280.04360.04520.12680.02340.02110.1894-0.00630.21427.4396-60.628457.87
330.9009-0.3135-0.07811.62530.39132.10660.0220.10160.0671-0.19490.0394-0.1906-0.05610.0903-0.06840.1358-0.00870.04660.1830.00660.20127.1077-47.087456.1047
340.9284-0.0332-0.06111.7582-0.14151.8205-0.0465-0.1369-0.08030.3247-0.002-0.16840.20510.25040.04630.20950.0237-0.02330.16380.01420.19531.8736-70.851674.9484
351.82470.4082-0.16253.04570.38392.2018-0.0108-0.1720.03180.46410.022-0.02010.11420.045-0.03270.34550.02730.01710.21560.02610.1744-4.3881-62.470286.386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 278 )
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 322 )
7X-RAY DIFFRACTION7chain 'A' and (resid 323 through 396 )
8X-RAY DIFFRACTION8chain 'A' and (resid 397 through 435 )
9X-RAY DIFFRACTION9chain 'A' and (resid 436 through 477 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 68 )
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 158 )
13X-RAY DIFFRACTION13chain 'B' and (resid 159 through 185 )
14X-RAY DIFFRACTION14chain 'B' and (resid 186 through 245 )
15X-RAY DIFFRACTION15chain 'B' and (resid 246 through 278 )
16X-RAY DIFFRACTION16chain 'B' and (resid 279 through 322 )
17X-RAY DIFFRACTION17chain 'B' and (resid 323 through 396 )
18X-RAY DIFFRACTION18chain 'B' and (resid 397 through 435 )
19X-RAY DIFFRACTION19chain 'B' and (resid 436 through 477 )
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 68 )
21X-RAY DIFFRACTION21chain 'C' and (resid 69 through 102 )
22X-RAY DIFFRACTION22chain 'C' and (resid 103 through 123 )
23X-RAY DIFFRACTION23chain 'C' and (resid 124 through 185 )
24X-RAY DIFFRACTION24chain 'C' and (resid 186 through 278 )
25X-RAY DIFFRACTION25chain 'C' and (resid 279 through 360 )
26X-RAY DIFFRACTION26chain 'C' and (resid 361 through 396 )
27X-RAY DIFFRACTION27chain 'C' and (resid 397 through 435 )
28X-RAY DIFFRACTION28chain 'C' and (resid 436 through 477 )
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 68 )
30X-RAY DIFFRACTION30chain 'D' and (resid 69 through 185 )
31X-RAY DIFFRACTION31chain 'D' and (resid 186 through 278 )
32X-RAY DIFFRACTION32chain 'D' and (resid 279 through 322 )
33X-RAY DIFFRACTION33chain 'D' and (resid 323 through 396 )
34X-RAY DIFFRACTION34chain 'D' and (resid 397 through 435 )
35X-RAY DIFFRACTION35chain 'D' and (resid 436 through 477 )

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