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- PDB-7lr1: Crystal structure of GH5_18 from Bifidobacterium longum subsp. lo... -

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Basic information

Entry
Database: PDB / ID: 7lr1
TitleCrystal structure of GH5_18 from Bifidobacterium longum subsp. longum ATCC 55813
ComponentsGlycosyl hydrolase BlGH5_18
KeywordsHYDROLASE / Glycosidase / N-glycan / CAZyme
Function / homologyGlycoside hydrolase superfamily / PHOSPHATE ION / Glycosyl hydrolase
Function and homology information
Biological speciesBifidobacterium longum subsp. longum ATCC 55813 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 15, 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase BlGH5_18
B: Glycosyl hydrolase BlGH5_18
C: Glycosyl hydrolase BlGH5_18
D: Glycosyl hydrolase BlGH5_18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,65147
Polymers198,4894
Non-polymers3,16243
Water42,1192338
1
A: Glycosyl hydrolase BlGH5_18
C: Glycosyl hydrolase BlGH5_18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,87324
Polymers99,2442
Non-polymers1,62922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-16 kcal/mol
Surface area29000 Å2
MethodPISA
2
B: Glycosyl hydrolase BlGH5_18
D: Glycosyl hydrolase BlGH5_18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,77823
Polymers99,2442
Non-polymers1,53421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-13 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.420, 143.730, 155.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Glycosyl hydrolase BlGH5_18


Mass: 49622.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum ATCC 55813 (bacteria)
Gene: HMPREF0175_1989 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C2GY91
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.22 M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→62.61 Å / Num. obs: 218071 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 16.26 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 10715 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LQX
Resolution: 1.8→55.48 Å / SU ML: 0.1538 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5739 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1726 10914 5.01 %
Rwork0.1388 207046 -
obs0.1405 217960 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13162 0 187 2338 15687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019813842
X-RAY DIFFRACTIONf_angle_d1.496118876
X-RAY DIFFRACTIONf_chiral_restr0.12341984
X-RAY DIFFRACTIONf_plane_restr0.01092464
X-RAY DIFFRACTIONf_dihedral_angle_d6.659910894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.22213680.19426920X-RAY DIFFRACTION100
1.82-1.840.23983590.19426776X-RAY DIFFRACTION100
1.84-1.860.23513750.18816851X-RAY DIFFRACTION100
1.86-1.890.21633980.17626813X-RAY DIFFRACTION100
1.89-1.910.22493760.17556843X-RAY DIFFRACTION100
1.91-1.940.21743330.17126876X-RAY DIFFRACTION100
1.94-1.970.18283630.1566819X-RAY DIFFRACTION100
1.97-20.19563860.15426850X-RAY DIFFRACTION99.99
2-2.030.19893360.15296888X-RAY DIFFRACTION100
2.03-2.060.19133490.14846860X-RAY DIFFRACTION100
2.06-2.10.18033720.14336867X-RAY DIFFRACTION100
2.1-2.130.16553750.13676851X-RAY DIFFRACTION99.99
2.13-2.180.16693220.13816901X-RAY DIFFRACTION100
2.18-2.220.18733490.13616863X-RAY DIFFRACTION100
2.22-2.270.17543500.13436869X-RAY DIFFRACTION100
2.27-2.320.16423530.13286961X-RAY DIFFRACTION100
2.32-2.380.17723370.13266850X-RAY DIFFRACTION100
2.38-2.440.16793620.12336921X-RAY DIFFRACTION100
2.44-2.510.15553580.12756895X-RAY DIFFRACTION100
2.51-2.60.17663450.13026903X-RAY DIFFRACTION100
2.6-2.690.16333580.13146911X-RAY DIFFRACTION100
2.69-2.80.17313290.13316945X-RAY DIFFRACTION100
2.8-2.920.16943680.14226930X-RAY DIFFRACTION100
2.92-3.080.17493860.1416903X-RAY DIFFRACTION100
3.08-3.270.16413810.13356933X-RAY DIFFRACTION99.97
3.27-3.520.1663910.13496947X-RAY DIFFRACTION99.93
3.52-3.880.15223670.12676969X-RAY DIFFRACTION99.84
3.88-4.440.14243880.11086963X-RAY DIFFRACTION99.72
4.44-5.590.14933910.127010X-RAY DIFFRACTION99.28
5.59-55.480.18213890.16327158X-RAY DIFFRACTION97.86
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)
12.186876494670.7035522005970.300950519230.993065563924-0.7658593158261.47768874665-0.1579914244290.1790049125790.113553611989-0.0286771486330.09795476237130.0744194342511-0.0907891157774-0.057658555059-0.02750712639160.09474617325940.00894074723917-0.03053829800930.0788265975235-0.0263606646930.098703737069165.176459183886.980047408484.2574684841
21.158851025680.111388281012-0.09705040378010.4589199731770.01668677435320.59423285664-0.0274449240046-0.02923207417310.188132936342-0.02574433471040.0553998530455-0.010827081101-0.1314063162270.063164435472-0.01800096222940.1407899213540.000617149445905-0.008922659407180.0863702945541-0.02734603733510.13957360626977.312215748695.422295882490.2625809313
32.82349516237-1.507061339350.8320305145034.06495404274-1.40727742492.94528828664-0.0268034928097-0.1759470642420.0230302380350.0819152979046-0.00278095756099-0.04934155279610.1958015824430.2483257344380.03135389465750.219348750937-0.006209749273040.006838850805820.192651047278-0.08595452871470.18504106703482.556705322696.9341160506105.491882918
40.5975514019360.102631001890.02549499685980.616656772783-0.03198675326290.704354733709-0.0296983174746-0.08922329739020.1295748399560.06556994031830.02804028671230.0729448337693-0.134102875771-0.0928482468527-0.005926397249920.1056705603370.04304590337810.002389017889860.11117141665-0.03089852873490.10954014180464.544197286586.6131042581104.632955665
52.8222984486-0.7212653396710.1408860163152.8341013499-0.2703441324782.13234583106-0.08034605983390.00272037309641-0.112522627734-0.00625401129980.05627226206590.2112419664350.00161546077115-0.1467287624750.03617689644060.06468498878620.0004371216405090.004066948494050.0849095008968-0.002133875924660.077163619085458.246274218778.208218179791.8676358553
60.5770641390020.0243387451624-0.1908447459040.9419761688930.3165546244930.9563855582890.0244902309137-0.1005969557640.1285069677660.11536285635-0.03967816998660.101086695248-0.142294644918-0.1517438973710.01475942273880.20500363560.05739207790920.02640736065530.192248759254-0.05845892367070.14368142889261.517755884689.7109558018118.040558259
70.985939310280.0259290157629-0.06299941830691.940888550090.7714340681391.37213968059-0.147954315423-0.3284046363110.2018478402840.3626397672250.1193588538970.181911624653-0.153739916126-0.1369909047980.004586564826820.2631843885330.08712915790470.03593979031470.242213745509-0.0813401969430.16177420752261.036084160191.4551970189123.169555747
83.080544681190.500485765189-0.227560861460.7678441724710.4316540192472.467406063880.10274759618-0.2983931615420.08220716744840.154916297379-0.0779456887456-0.0443057107599-0.09131236958030.0684454145319-0.03746951976120.09321308888040.000674643472435-0.0141532878920.0797928485271-0.008416479670630.091431066188482.644392229891.821566883452.2620164349
91.519419451790.378520817626-0.1540473947850.605112069205-0.1270733752140.5757502943880.0287045449682-0.06965249997620.1263957817280.0388772342631-0.002396832854890.0709598477139-0.0888119570319-0.0300944597685-0.02615709271650.1334191837660.01484204023490.005602606862710.1006017528960.01182542259820.11084480187871.711706382592.129065128549.1522363411
101.017622479950.329511963228-0.0558582099890.495722302412-0.474286419971.089007356720.01888682197620.128565930770.10834474912-0.04869491462550.04991494573880.08545471768530.0090081780926-0.151188485374-0.05278372336580.138746701470.04095374736690.004424241332110.1412249621050.0351087254850.14675419945462.998606084591.551756115338.5148244376
110.659075419674-0.111041339772-0.1614111106610.564828730919-0.06529051673330.9166038817780.04838720502660.02316269911250.0938004649801-0.0172059659093-0.02628041496490.0015894564666-0.1164888582740.0411283104232-0.0120170186460.0947547739154-0.002961164956630.007977614354750.07383054771710.01347707071260.08311308653284.521099969390.56484200433.7103629814
120.633817242463-0.1043455013280.2418135394180.626454156274-0.4613583883662.064840741880.0329516285020.093763298880.204960013177-0.0913421355866-0.0617056948664-0.0507168958676-0.225171102110.1160977551120.05155179380340.147775193260.01926389206170.03340152577120.1108047823640.03869709220640.14191724348886.801733697296.895274337422.1841595943
131.566528642220.39552926730.409980887164.79773682152-0.5621167117461.89967639993-0.01847857688160.1604616150020.207962597764-0.4608137901280.04036934622020.142715393975-0.1582789158860.0481735392633-0.03469339559850.2106975010340.04464955258780.02388880095530.1819788601950.04109690589810.13370701429883.530132649395.917375478411.90955762
141.040991020720.131992729178-0.288921803990.542996449308-0.3624835078541.13859005545-0.06253191429430.0600263513943-0.00228825870844-0.04595854368710.03072484213020.00694911552551-0.01132205184860.01434851169930.0364351340550.0977139658116-0.01320654980740.0008426911887590.103041131131-0.0155901199040.095633965227294.137429646582.336369129975.6960202036
151.33331871216-0.00665113328902-0.181934235780.576202151719-0.1847532287030.539512204074-0.0945594993362-0.09609882494380.003031932144910.01644277391690.0407536447616-0.0771875786946-0.02918596722790.1224756057990.0569683528430.0962054682857-0.005733062156140.00138779911730.153890841452-0.01595956871030.108029195012111.6756880881.847924143980.3267061808
162.00708596690.273993699982-1.459130771072.510640061351.298512290776.049325012310.0697094511470.09243478787380.433130352353-0.2159160997460.158955583181-0.0827890285127-0.4993542861540.188090170653-0.2132164383590.137607665384-0.0605259389618-0.01545546621650.1378052922350.03332792908640.195825015922109.35188046597.826281757670.8208114127
171.51308858421-0.360207210091-0.1289651730441.22432736691-0.0593375958430.809319126214-0.067267942338-0.170001923321-0.101154945704-0.01297967201710.05252377909750.0138682261323-0.02402296158330.1560988444720.02012274246370.09254742132180.00769670468773-0.0023242291980.23887068788-0.01114940721430.160681295272125.05063677276.297124173882.1730746559
182.32180174261-0.198347626531-0.1954295394641.875300787910.3422472631172.04309148963-0.158017563344-0.274366301702-0.1379197482030.0559675614880.114632459863-0.0464645713607-0.01328270643490.09730926912090.03333890337140.08289389346690.01301334657480.00307586091180.272144707526-0.01085679267510.177219450801126.09522129775.147612336684.5423111607
191.336132028490.814052876137-0.8606841334530.975214783589-0.5485031385551.457326746690.0518489328466-0.1477503795630.09818626960320.0202855088348-0.04378068588170.0732080548231-0.05298078106070.0285280984163-0.02374649348620.0851561138550.01397521718870.006009796115990.106773020661-0.01402186017610.10903404084553.017653747778.674463812167.613149075
200.9494287953220.160040711517-0.47564766850.41790479909-0.02312270615141.18609355071-0.03076466953970.0196563836611-0.00842297477728-0.0483492358244-0.00868610846207-0.02131026127180.02184998833820.04796082167280.03773748217660.08573590119980.000676225637153-0.003767500471340.07755597258290.003024354302920.095113572208762.783387675272.561807029158.0734233172
210.7491084130990.176420048215-0.4840758659220.6977902001150.6661793959313.08190584852-0.0439818375161-0.0723686410355-0.058540667997-0.01804693791580.0109322768198-0.09384513123530.1014183672680.1446926820520.03437298434340.1344754586180.01550318520890.01069432231850.09621945819650.01684061820510.12970543771565.426421242465.245294450259.6068370434
220.9571715098870.206961619928-0.4485916274550.913399681886-0.1165450343790.807305646673-0.08565427666640.112839091483-0.088879390725-0.1330928059910.02397002389410.05964095565050.131332245168-0.1459249324430.05712257910870.119718398325-0.0357293400431-0.0116620682770.118223825077-0.02451890864540.10380778821146.382613574462.339797986156.413030186
230.8436593522880.0163078848574-0.2256060779070.9809395148271.401301336862.280267225450.0631449176747-0.009425488599590.05637923122940.2540961245580.03965556734460.18907777619-0.0777635999245-0.254205681715-0.06054528391890.0371455400198-0.00220383138152-0.01113446791120.131648798178-0.01457194141570.13577553267439.395948877671.153625760167.5065137948
240.2457010885610.140461792199-0.2650662179161.145954318910.09727981792160.737974630246-0.255920758180.345965026069-0.114947344586-0.3554664242640.1298333582250.06470784331430.266924792455-0.3107796023480.1234417416610.282767638066-0.1341925402530.01345949623470.240001190184-0.09243999775790.21160629747638.338114202349.556693324750.0071247775
251.279794447420.09334865657410.04388955292811.594258164990.7655047956841.38286410277-0.2452665068320.205409127859-0.141010620201-0.2506667956150.218571029270.1017231171190.316456040478-0.2191076018720.04841537764440.262431197672-0.125260408383-0.003702061208730.23792933594-0.08131356832020.21435237734737.804543946948.728482924852.3571341422
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 34 )AA-1 - 34-1 - 34
22chain 'A' and (resid 35 through 144 )AA35 - 14435 - 144
33chain 'A' and (resid 145 through 171 )AA145 - 171145 - 171
44chain 'A' and (resid 172 through 302 )AA172 - 302172 - 302
55chain 'A' and (resid 303 through 331 )AA303 - 331303 - 331
66chain 'A' and (resid 332 through 375 )AA332 - 375332 - 375
77chain 'A' and (resid 376 through 417 )AA376 - 417376 - 417
88chain 'B' and (resid -1 through 34 )BB-1 - 34-1 - 34
99chain 'B' and (resid 35 through 94 )BB35 - 9435 - 94
1010chain 'B' and (resid 95 through 171 )BB95 - 17195 - 171
1111chain 'B' and (resid 172 through 318 )BB172 - 318172 - 318
1212chain 'B' and (resid 319 through 388 )BB319 - 388319 - 388
1313chain 'B' and (resid 389 through 416 )BB389 - 416389 - 416
1414chain 'C' and (resid -1 through 145 )CC - B-1 - 145-1 - 145
1515chain 'C' and (resid 146 through 302 )CC146 - 302146 - 302
1616chain 'C' and (resid 303 through 331 )CC303 - 331303 - 331
1717chain 'C' and (resid 332 through 375 )CC332 - 375332 - 375
1818chain 'C' and (resid 376 through 422 )CC376 - 422376 - 422
1919chain 'D' and (resid -1 through 34 )DD-1 - 34-1 - 34
2020chain 'D' and (resid 35 through 108 )DD35 - 10835 - 108
2121chain 'D' and (resid 109 through 145 )DD109 - 145109 - 145
2222chain 'D' and (resid 146 through 302 )DD146 - 302146 - 302
2323chain 'D' and (resid 303 through 341 )DD303 - 341303 - 341
2424chain 'D' and (resid 342 through 375 )DD342 - 375342 - 375
2525chain 'D' and (resid 376 through 422 )DD376 - 422376 - 422

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