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- PDB-5y3x: Crystal structure of endo-1,4-beta-xylanase from Caldicellulosiru... -

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Basic information

Entry
Database: PDB / ID: 5y3x
TitleCrystal structure of endo-1,4-beta-xylanase from Caldicellulosiruptor owensensis
ComponentsBeta-xylanase
KeywordsHYDROLASE / GH10 xylanase / Thermostability
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaldicellulosiruptor owensensis OL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, X. / Sun, L.C. / Zhang, Y.B. / Liu, T.F. / Xin, F.J.
Funding support China, 2items
OrganizationGrant numberCountry
modern food processing and food storage and transportation technology and equipment2017YFD0400200 China
National Natural Science Foundation of China31571963 China
CitationJournal: J. Agric. Food Chem. / Year: 2018
Title: Structural Insights into the Thermophilic Adaption Mechanism of Endo-1,4-beta-Xylanase from Caldicellulosiruptor owensensis.
Authors: Liu, X. / Liu, T. / Zhang, Y. / Xin, F. / Mi, S. / Wen, B. / Gu, T. / Shi, X. / Wang, F. / Sun, L.
History
DepositionJul 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
C: Beta-xylanase
D: Beta-xylanase
E: Beta-xylanase
F: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)254,5636
Polymers254,5636
Non-polymers00
Water20,1951121
1
A: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4271
Polymers42,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4271
Polymers42,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4271
Polymers42,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4271
Polymers42,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4271
Polymers42,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta-xylanase


Theoretical massNumber of molelcules
Total (without water)42,4271
Polymers42,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.650, 74.071, 137.744
Angle α, β, γ (deg.)90.000, 90.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-xylanase


Mass: 42427.133 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor owensensis OL (bacteria)
Strain: ATCC 700167 / DSM 13100 / OL / Gene: Calow_0124 / Production host: Escherichia coli (E. coli) / References: UniProt: E4Q2A4, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1121 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 5% Iso-Propanol, 2.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.1→29.113 Å / Num. obs: 148527 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
PDB_EXTRACT3.22data extraction
HKL-3000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PMD

4pmd


Resolution: 2.1→29.113 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 7446 5.01 %
Rwork0.1897 --
obs0.1916 148526 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.65 Å2 / Biso mean: 36.3408 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 2.1→29.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16626 0 0 1121 17747
Biso mean---39.45 -
Num. residues----1974
LS refinement shellResolution: 2.0998→2.1237 Å / Total num. of bins used: 30 /
RfactorNum. reflection
Rfree0.2667 241
Rwork0.223 4442
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)
10.3764-0.2816-0.31710.26290.15360.36580.22980.33370.1014-0.5263-0.3319-0.0081-0.6313-0.25330.14820.34360.4242-0.0253-0.07260.12060.2449-73.861510.9956-82.571
20.5366-0.5373-0.21631.6105-0.1750.66620.06970.07440.0756-0.0886-0.095-0.3548-0.16880.0267-0.00680.20910.02960.0130.1083-0.0020.279-62.2487.1303-67.9514
30.671-0.0019-0.11280.8130.14310.65740.06850.02510.02990.0548-0.1530.03050.0162-0.10930.0240.16540.02830.02840.1077-0.02260.1618-72.75921.6414-64.2506
40.3008-0.0787-0.43860.48570.21940.5890.13180.2666-0.1683-0.2487-0.38780.28-0.0451-0.54480.08670.18990.1069-0.0520.3585-0.09870.1951-80.5169-6.7097-83.9079
51.6901-0.41130.02430.66330.09580.83940.0288-0.14030.22110.2205-0.0241-0.2357-0.30260.1452-0.01520.2494-0.094-0.03970.29560.0180.3046-99.7033.9227-54.2708
60.8986-0.44230.79920.3755-0.49471.96810.0857-0.18220.20120.21780.01040.0766-0.0567-0.2226-0.02650.2327-0.00650.03090.2188-0.02580.2344-115.98246.5728-53.1354
73.75310.14491.73431.10720.16922.34050.0303-0.07010.26790.1318-0.10010.1043-0.3566-0.36210.11380.26840.0120.06280.2172-0.03210.2667-123.581214.4688-59.8359
80.54140.0009-0.15071.17720.1061.13030.15580.09220.1659-0.0002-0.09040.2013-0.0502-0.30820.04570.15170.03790.01760.21560.00970.2621-125.947.6435-71.7757
91.41140.82170.25042.98310.42281.18670.0868-0.0040.09550.0436-0.114-0.04090.1503-0.12310.01690.13850.00140.02720.24280.0510.1376-117.7516-2.6018-71.7438
100.6747-0.58480.15491.09470.88251.84890.07750.21590.0848-0.2938-0.22020.0077-0.0567-0.07540.02210.17020.0427-0.0030.31170.04290.2136-121.58913.1973-80.006
110.735-0.2537-0.25471.9895-0.7871.50720.03040.13870.02840.0187-0.0393-0.10860.1365-0.02050.01460.1318-0.00120.02790.19720.0110.1576-110.7522-5.7684-74.9642
120.61280.2384-0.17070.8472-0.39721.97020.0970.1033-0.042-0.0841-0.0184-0.03560.190.01860.00940.1510.003-0.00710.19730.01220.1777-106.141-8.2286-66.527
131.74930.8157-0.59050.7854-0.29520.6865-0.0352-0.2548-0.10440.0194-0.0492-0.17590.29420.04110.01620.2047-0.0357-0.01310.21990.00980.1703-107.8861-14.9423-50.8867
140.82850.1917-0.07950.94380.0280.85660.1183-0.11120.02170.1929-0.0907-0.0583-0.0794-0.1763-0.01750.2168-0.0331-0.01190.25620.00110.1648-109.454-5.4858-50.6259
150.50660.0648-0.07040.43880.14261.14310.04350.0752-0.0828-0.18060.02640.12140.1548-0.27670.05320.3402-0.0457-0.05630.1451-0.01410.2473-90.4977-21.7468-36.4705
160.93440.7350.50690.74910.09731.64410.007-0.10520.3008-0.0372-0.02570.32850.0118-0.27120.03550.1872-0.02330.01340.1197-0.00150.2825-93.703-9.4224-22.4402
170.83280.034-0.08340.541-0.01650.9510.0317-0.1477-0.06560.0195-0.0343-0.0070.0790.0527-0.00410.2149-0.0105-0.01630.11180.01350.174-81.3656-16.5147-19.3952
180.44010.09540.0070.9137-0.33890.6389-0.05710.1043-0.0947-0.05590.0264-0.08690.12180.14090.03980.27790.0304-0.01920.1475-0.01060.1822-72.3525-16.9391-41.3349
190.64810.71110.22011.13150.6060.4498-0.0555-0.1121-0.42760.07390.00130.05150.3155-0.09660.01520.5606-0.01180.02770.24010.07770.4238-108.0204-32.8069-100.4869
200.81770.0372-0.3360.8697-0.57771.6721-0.0676-0.35680.08580.1820.0094-0.2116-0.00970.2364-0.00720.27750.0832-0.02790.2739-0.02540.2751-94.0416-18.2375-101.9458
211.1793-0.77010.46810.58550.04411.80960.00590.10350.2895-0.1308-0.0792-0.196-0.06560.20170.03930.17110.06110.05320.14620.0220.2723-95.1486-9.1063-115.6092
221.28040.10560.03110.6155-0.14891.32360.05670.3122-0.0537-0.1636-0.0548-0.07160.1988-0.1543-0.04230.22880.04090.03120.2098-0.03210.1685-102.7401-15.4176-121.2375
230.837-0.244-0.49720.52120.16951.27710.0160.0826-0.31-0.0291-0.05030.10980.3325-0.4874-0.0340.2814-0.0911-0.00710.3603-0.0410.2809-116.1894-21.4187-112.5738
240.3322-0.0301-0.0192.07281.05730.9266-0.041-0.1643-0.1696-0.1215-0.0090.09660.1175-0.53750.1040.2808-0.054-0.02380.45440.02230.2888-121.2873-16.9292-97.0571
250.727-0.0583-0.10720.82860.18091.1828-0.1383-0.3838-0.19820.14230.15920.01850.2172-0.1980.03120.3205-0.01080.01810.36230.05240.2634-112.1981-20.0234-96.6861
260.65640.2283-0.31281.3841-0.48490.259-0.07870.44430.2621-0.1588-0.0444-0.2811-0.11750.3114-0.06310.2674-0.121-0.05350.71880.16640.4046-50.7823-4.8316-129.9126
270.23020.2227-0.35940.8379-0.63551.62310.14810.5704-0.1073-0.2735-0.0663-0.07490.18590.25540.05860.21040.09340.02390.5942-0.0420.225-56.9573-20.1488-130.7658
281.30990.8236-0.51252.0929-0.71271.6139-0.03130.41-0.2508-0.1668-0.0768-0.17120.40050.13130.1350.22910.172-0.00850.4035-0.11630.2475-54.0029-30.6856-123.7341
290.8438-0.53240.30430.64930.3180.9060.05460.0398-0.24250.0341-0.06830.15690.24860.19680.02890.22910.045-0.01350.20520.00980.3027-63.7808-28.159-113.9609
300.7422-0.31210.30870.9932-0.06360.8376-0.0462-0.0009-0.01020.226-0.0181-0.0499-0.06640.05630.01940.18590.0297-0.0270.1635-0.00810.1854-62.5841-18.143-108.5754
310.460.04780.40320.3511-0.00140.8815-0.17710.03120.1990.09290.0341-0.1217-0.25580.07450.08540.2697-0.0074-0.06190.20470.02920.2575-64.4851-3.8363-117.5224
321.08250.27471.0310.43380.27450.991-0.1596-0.05320.2008-0.1331-0.1413-0.1056-0.39440.09030.17960.2712-0.0183-0.04660.21590.01580.2353-70.8726-1.9033-132.4784
330.8594-0.11260.28190.67310.0641.23640.04470.52680.04010.0213-0.0621-0.17690.04760.47160.14570.19640.0015-0.01290.43640.06620.1945-64.1069-8.669-133.7998
340.4940.004-0.18690.8365-0.41520.8045-0.00820.1099-0.0107-0.19930.0601-0.21360.07870.4198-0.0010.1955-0.01640.05690.5892-0.07930.2453-118.290420.8645-129.8952
351.76280.548-0.42361.3806-0.27021.4592-0.08350.0865-0.1693-0.17550.141-0.10820.33360.01580.08750.21120.09220.01290.5163-0.09040.2444-117.77834.8677-123.7019
361.5237-0.6991-0.12620.43410.46791.5044-0.0346-0.18-0.0495-0.00440.00640.20720.2947-0.00860.0250.12570.11330.00110.4983-0.0130.2155-127.78077.1091-114.0611
370.6644-0.2288-0.05051.0161-0.0010.4607-0.1753-0.22680.04560.21750.2281-0.15010.00740.2727-0.02560.17050.0951-0.02640.4708-0.05810.1746-126.651916.8554-108.384
380.9803-0.2140.74710.8245-0.18121.61620.004-0.14310.2827-0.0420.3042-0.1483-0.15340.1447-0.07280.2166-0.0331-0.00840.4572-0.08020.2337-129.194332.3858-115.1982
390.80320.02230.22210.56470.23350.91870.10180.16230.2268-0.05740.0899-0.0767-0.25850.2469-0.14360.2837-0.07980.05880.4295-0.03340.2395-129.870529.699-131.3269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 78 )A9 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 108 )A79 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 224 )A109 - 224
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 337 )A225 - 337
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 26 )B9 - 26
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 57 )B27 - 57
7X-RAY DIFFRACTION7chain 'B' and (resid 58 through 78 )B58 - 78
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 127 )B79 - 127
9X-RAY DIFFRACTION9chain 'B' and (resid 128 through 152 )B128 - 152
10X-RAY DIFFRACTION10chain 'B' and (resid 153 through 173 )B153 - 173
11X-RAY DIFFRACTION11chain 'B' and (resid 174 through 205 )B174 - 205
12X-RAY DIFFRACTION12chain 'B' and (resid 206 through 251 )B206 - 251
13X-RAY DIFFRACTION13chain 'B' and (resid 252 through 286 )B252 - 286
14X-RAY DIFFRACTION14chain 'B' and (resid 287 through 337 )B287 - 337
15X-RAY DIFFRACTION15chain 'C' and (resid 9 through 78 )C9 - 78
16X-RAY DIFFRACTION16chain 'C' and (resid 79 through 108 )C79 - 108
17X-RAY DIFFRACTION17chain 'C' and (resid 109 through 251 )C109 - 251
18X-RAY DIFFRACTION18chain 'C' and (resid 252 through 337 )C252 - 337
19X-RAY DIFFRACTION19chain 'D' and (resid 9 through 26 )D9 - 26
20X-RAY DIFFRACTION20chain 'D' and (resid 27 through 78 )D27 - 78
21X-RAY DIFFRACTION21chain 'D' and (resid 79 through 108 )D79 - 108
22X-RAY DIFFRACTION22chain 'D' and (resid 109 through 205 )D109 - 205
23X-RAY DIFFRACTION23chain 'D' and (resid 206 through 251 )D206 - 251
24X-RAY DIFFRACTION24chain 'D' and (resid 252 through 286 )D252 - 286
25X-RAY DIFFRACTION25chain 'D' and (resid 287 through 337 )D287 - 337
26X-RAY DIFFRACTION26chain 'E' and (resid 9 through 26 )E9 - 26
27X-RAY DIFFRACTION27chain 'E' and (resid 27 through 57 )E27 - 57
28X-RAY DIFFRACTION28chain 'E' and (resid 58 through 78 )E58 - 78
29X-RAY DIFFRACTION29chain 'E' and (resid 79 through 108 )E79 - 108
30X-RAY DIFFRACTION30chain 'E' and (resid 109 through 205 )E109 - 205
31X-RAY DIFFRACTION31chain 'E' and (resid 206 through 251 )E206 - 251
32X-RAY DIFFRACTION32chain 'E' and (resid 252 through 287 )E252 - 287
33X-RAY DIFFRACTION33chain 'E' and (resid 288 through 337 )E288 - 337
34X-RAY DIFFRACTION34chain 'F' and (resid 9 through 57 )F9 - 57
35X-RAY DIFFRACTION35chain 'F' and (resid 58 through 78 )F58 - 78
36X-RAY DIFFRACTION36chain 'F' and (resid 79 through 108 )F79 - 108
37X-RAY DIFFRACTION37chain 'F' and (resid 109 through 204 )F109 - 204
38X-RAY DIFFRACTION38chain 'F' and (resid 205 through 239 )F205 - 239
39X-RAY DIFFRACTION39chain 'F' and (resid 240 through 337 )F240 - 337

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