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- PDB-7lr7: Crystal structure of GH5_18 from Streptomyces cattleya in complex... -

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Basic information

Entry
Database: PDB / ID: 7lr7
TitleCrystal structure of GH5_18 from Streptomyces cattleya in complex with GlcNAc
ComponentsUncharacterized protein ScGH5_18
KeywordsHYDROLASE / Glycosidase / N-glycan / CAZyme
Function / homologyGlycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 2-(2-ETHOXYETHOXY)ETHANOL / Glycosyl hydrolase
Function and homology information
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHiggins, M.A. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: N-Glycan Degradation Pathways in Gut- and Soil-Dwelling Actinobacteria Share Common Core Genes.
Authors: Higgins, M.A. / Tegl, G. / MacDonald, S.S. / Arnal, G. / Brumer, H. / Withers, S.G. / Ryan, K.S.
History
DepositionFeb 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Uncharacterized protein ScGH5_18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3344
Polymers47,9161
Non-polymers4173
Water6,197344
1
A: Uncharacterized protein ScGH5_18
hetero molecules

A: Uncharacterized protein ScGH5_18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6688
Polymers95,8332
Non-polymers8356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5030 Å2
ΔGint2 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.151, 115.761, 159.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-917-

HOH

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Components

#1: Protein Uncharacterized protein ScGH5_18


Mass: 47916.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057) (bacteria)
Strain: ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057
Gene: SCATT_p07120 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F8JJ04
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 3350, 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→79.79 Å / Num. obs: 32258 / % possible obs: 99.7 % / Redundancy: 12 % / Biso Wilson estimate: 22.98 Å2 / CC1/2: 0.994 / Net I/σ(I): 8.4
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2207 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LQX

7lqx


Resolution: 1.95→48.33 Å / SU ML: 0.2651 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4077 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2202 1538 4.77 %
Rwork0.17 30711 -
obs0.1723 32249 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.79 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 28 344 3582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693354
X-RAY DIFFRACTIONf_angle_d0.84344604
X-RAY DIFFRACTIONf_chiral_restr0.0545505
X-RAY DIFFRACTIONf_plane_restr0.0049608
X-RAY DIFFRACTIONf_dihedral_angle_d6.85731937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.38681270.29622721X-RAY DIFFRACTION99.27
2.01-2.080.28551500.25812734X-RAY DIFFRACTION99.38
2.08-2.170.31511200.2172807X-RAY DIFFRACTION99.9
2.17-2.270.23411630.19982737X-RAY DIFFRACTION99.9
2.27-2.390.21861360.17872756X-RAY DIFFRACTION99.79
2.39-2.540.19691320.16632782X-RAY DIFFRACTION99.15
2.54-2.730.21071470.162763X-RAY DIFFRACTION99.59
2.73-3.010.22131450.16662786X-RAY DIFFRACTION99.9
3.01-3.440.2241470.15472792X-RAY DIFFRACTION99.56
3.44-4.340.16751370.13352865X-RAY DIFFRACTION99.87
4.34-48.330.20291340.15372968X-RAY DIFFRACTION99.23
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)
10.428557114362-0.328117360499-0.3416029725013.77893585248-0.51244310020.7690419461570.000156327782690.2112770796540.0317994568556-0.0578826795060.0692350029618-0.0463913212519-0.0764597338489-0.0631495715059-0.07104845953460.1306594171320.0147952078127-0.002500100637760.2328378293190.04831943686810.1287607986794.4465830542714.305057393245.9389452626
23.514141212560.66059630209-1.811659675132.48817421363-0.9369580414343.458007188210.01787331887820.14452593690.0818220890643-0.0855188655531-0.00800061798334-0.0414661860481-0.1092744655080.0695821831881-0.01932799241690.1170115149940.0259359803143-0.02344581613950.1465487409530.02815511282370.1482659954396.9582561314612.126700945646.4606018152
30.6794114482510.286395882006-0.2072691285611.86285772121-0.8651509054441.795772040270.03609204840130.06770180581020.1099322718030.168615976327-0.0739849586784-0.19402465623-0.004568540785390.1231218211790.06153331310950.1537314382430.0244571106586-0.01752169916050.214920501601-0.003943167515610.17945259389712.63704071880.89911607746159.2169006596
42.128161592291.12138886661-2.22013735142.1147269938-1.72180527527.05530336322-0.04097566839140.2592168921510.204630530138-0.2173227017790.129845747728-0.1418253083590.22279841921-0.101316299669-0.1560550535860.1489271024980.03982816924170.01701642317360.1901094436160.04131687983460.18147961209512.763558176514.51127599152.2472818114
51.904985813041.47397299668-1.427573889411.60971204206-0.9940219787735.977219168097.05770803038E-5-0.198559921816-0.1653191531270.267603310977-0.150378331145-0.2508112139060.06433870348590.3821702960660.1446492112480.1971242296180.036582120515-0.0121976870240.1162086192590.02001423510090.19071192235615.53336385269.591792876165.6950393793
64.90022207436-1.59765461284-2.733807799423.133166041551.663411422952.08759683335-0.0121817995464-0.008292363252040.2539874563340.2308696785440.0755464748918-0.1517451054320.07335048534850.010339449519-0.08794864906950.173065553402-0.00978877598905-0.04603542031750.122162396770.001039459747340.1908129141814.251966113920.234050349863.8569549396
73.026045861252.284413892151.248244992552.22488718210.2372011296172.01585290576-0.0689578608714-0.005535512505470.1479794716080.2109018042120.04854997055110.252158519273-0.203294753816-0.1621838117090.01935154825390.244972010070.04010345912280.02428422495920.155733669596-0.006994440760770.2160875166523.4347222861932.132008026166.5162450507
84.611761315-0.2356656991051.485734373672.94298649421-0.6103076910642.430419582190.0313501646445-0.02761191221260.2892311350430.0646140716221-0.06288223275160.0128577626021-0.247359585063-0.10056607410.04224051868590.199704376830.01373919370920.025490067160.140926945970.01722064065220.1613717328324.3293767335831.991124604757.5942459165
91.254219791571.53849204044-0.7288317068332.49703595368-0.3917677467520.953136449012-0.1220776964170.09461856248930.0714166955672-0.1360420621960.00453810433195-0.119608087605-0.019637248556-0.03778506003420.1131763104540.1651993586910.0373259151103-0.01961009364140.1743635098420.0578394608470.219543962962-0.37026168794722.295414341352.8044701931
104.276076812762.28277931304-0.3004327890853.219811089140.1991737263691.02226845414-0.09044654052230.2637108868560.370939601356-0.2563675432330.08681697225520.168184462855-0.1018505812680.0381291341236-0.005881489411520.2098780525210.0560419202949-0.003195251721330.2000864173310.0673446230360.216937452278-3.2807756583429.723418788647.0149137784
112.57190702431.85295639106-0.5759615789812.68442339853-0.1861590725965.79240168746-0.0112737640086-0.01813722133980.363970015830.1422760380550.003552131791180.0255029643679-0.3510432072380.1407178166810.05074090765930.1865259091730.0314184501412-0.03535312920720.159581563491-0.01603896344230.26094031799412.172149022335.952367446970.1488470212
124.42769720483-0.594012669272-6.440036748881.153542303430.1731387674549.83291909051-0.04836985971240.763470407904-1.0248643225-0.287191311212-0.061495679582-0.0329481183204-0.0207072258808-0.2761957486080.2243970883750.245367644473-0.0254453548928-0.07028951197990.294635261816-0.04295005584440.35859581189325.220018598134.076834507475.7909589607
137.549448560033.535809925732.431480256099.848676435442.722775210729.67213879175-0.199417703286-0.08171111368620.0488742914418-0.17346032771-0.21701328338-0.7015324282010.0639719275660.6858710224860.2663508082980.322418439929-0.0554196381614-0.02263754931640.271538550120.02663888518210.31048587955427.365528616237.758361467268.239902095
144.09604259171-0.9079487342142.06944769017.02967092257-2.040997761459.31873530732-0.2327766945150.1345966377950.7236922957470.2313510347060.3992460005140.769649813664-0.7824668452380.233248040029-0.1597892452660.367997822954-0.0420188131312-0.08089701010050.183213021670.0361892787220.39255856342719.999333932142.94637451972.4542408002
155.373196148-3.703668520873.659368758388.33129065906-2.668688386252.51100068527-0.84247197259-1.832765851611.211404030490.260996524121-0.1741131793750.977571785538-1.62929889782-0.8757932450640.8804919544350.4765258046620.0929530252411-0.1824137490830.602010881726-0.1451046607730.60356032822910.55436583342.827812455881.0853648995
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 70 )10 - 7010 - 70
22chain 'A' and (resid 71 through 105 )71 - 10571 - 105
33chain 'A' and (resid 106 through 139 )106 - 139106 - 139
44chain 'A' and (resid 140 through 157 )140 - 157140 - 157
55chain 'A' and (resid 158 through 187 )158 - 187158 - 187
66chain 'A' and (resid 188 through 225 )188 - 225188 - 225
77chain 'A' and (resid 226 through 256 )226 - 256226 - 256
88chain 'A' and (resid 257 through 294 )257 - 294257 - 294
99chain 'A' and (resid 295 through 317 )295 - 317295 - 310
1010chain 'A' and (resid 318 through 348 )318 - 348318 - 348
1111chain 'A' and (resid 349 through 400 )349 - 400349 - 400
1212chain 'A' and (resid 401 through 406 )401 - 406401 - 406
1313chain 'A' and (resid 407 through 413 )407 - 413407 - 413
1414chain 'A' and (resid 414 through 420 )414 - 420414 - 420
1515chain 'A' and (resid 421 through 425 )421 - 425421 - 425

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