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- PDB-7k1r: X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 ... -

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Basic information

Entry
Database: PDB / ID: 7k1r
TitleX-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 F507A mutant
ComponentsBeta xylosidase GH43
KeywordsHYDROLASE / Glycoside Hydrolase / GH43 / Beta-xylosidase / Enterobacter
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesEnterobacter sp. enrichment culture clone nf1B6 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBriganti, L. / Capetti, C.C.M. / Polikarpov, I.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/13684-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)423693/2016-6 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303988/2016-9 Brazil
CitationJournal: To Be Published
Title: X-ray Structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 F507A mutant
Authors: Briganti, L. / Capetti, C.C.M. / Polikarpov, I.
History
DepositionSep 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta xylosidase GH43
B: Beta xylosidase GH43
C: Beta xylosidase GH43
D: Beta xylosidase GH43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,04410
Polymers243,6994
Non-polymers3456
Water25,1311395
1
A: Beta xylosidase GH43
D: Beta xylosidase GH43
hetero molecules

B: Beta xylosidase GH43
hetero molecules

C: Beta xylosidase GH43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,04410
Polymers243,6994
Non-polymers3456
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area11220 Å2
ΔGint-93 kcal/mol
Surface area70020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.123, 153.100, 182.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Beta xylosidase GH43


Mass: 60924.859 Da / Num. of mol.: 4 / Mutation: F507A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. enrichment culture clone nf1B6 (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: V5J3M5, xylan 1,4-beta-xylosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1395 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 4M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.4→49.15 Å / Num. obs: 95985 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 37.98 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.08 / Rrim(I) all: 0.291 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) all% possible allRmerge(I) obsRrim(I) all
2.4-2.4411.846190.390.77798.2
2.4-49.1510.66760.9980.02598.30.0850.089

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASER1.14-3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EXH
Resolution: 2.4→22.72 Å / SU ML: 0.3032 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2275 4608 4.81 %
Rwork0.19 91143 -
obs0.1918 95751 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→22.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17109 0 16 1395 18520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002117720
X-RAY DIFFRACTIONf_angle_d0.570724208
X-RAY DIFFRACTIONf_chiral_restr0.04372460
X-RAY DIFFRACTIONf_plane_restr0.00393151
X-RAY DIFFRACTIONf_dihedral_angle_d5.69382374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.33411470.31392927X-RAY DIFFRACTION97.37
2.43-2.460.31681400.28713010X-RAY DIFFRACTION100
2.46-2.490.31731500.28523030X-RAY DIFFRACTION99.97
2.49-2.520.34791530.28422972X-RAY DIFFRACTION100
2.52-2.550.30691640.28823010X-RAY DIFFRACTION100
2.55-2.590.27391560.28243017X-RAY DIFFRACTION100
2.59-2.620.31991190.2743015X-RAY DIFFRACTION100
2.62-2.660.3031300.25523042X-RAY DIFFRACTION100
2.66-2.70.30521700.26143002X-RAY DIFFRACTION99.97
2.7-2.750.30761690.25542959X-RAY DIFFRACTION100
2.75-2.790.27391710.25173032X-RAY DIFFRACTION100
2.79-2.840.28841550.25253013X-RAY DIFFRACTION100
2.84-2.90.29621620.24473032X-RAY DIFFRACTION100
2.9-2.960.28391500.24192987X-RAY DIFFRACTION100
2.96-3.020.24651390.23463048X-RAY DIFFRACTION100
3.02-3.090.30161570.22923034X-RAY DIFFRACTION100
3.09-3.170.26961570.22192986X-RAY DIFFRACTION100
3.17-3.260.24421570.20973050X-RAY DIFFRACTION100
3.26-3.350.2211490.19483037X-RAY DIFFRACTION100
3.35-3.460.21011580.18273044X-RAY DIFFRACTION100
3.46-3.580.20311550.16643015X-RAY DIFFRACTION100
3.58-3.720.1931560.15323043X-RAY DIFFRACTION99.97
3.72-3.890.20551650.15513045X-RAY DIFFRACTION100
3.89-4.10.19281530.14323056X-RAY DIFFRACTION99.94
4.1-4.350.16121530.13523071X-RAY DIFFRACTION100
4.35-4.690.17791450.133077X-RAY DIFFRACTION99.91
4.69-5.150.1421480.12553101X-RAY DIFFRACTION99.97
5.15-5.890.20161460.15593114X-RAY DIFFRACTION99.97
5.89-7.370.18921470.16673145X-RAY DIFFRACTION100
7.38-22.720.21161870.18023229X-RAY DIFFRACTION99.56
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)
11.243493779280.300838997949-0.1249127321791.56659199028-0.3175196504430.665873080657-0.09709674359930.1528441241880.091740286158-0.1529505012210.0442899428911-0.01838271972370.101066589955-0.1310535619230.06142859602430.2693276147430.00186377873362-0.003616607973510.332227863464-0.004043542333260.27462021655916.043324340363.441748425371.4480448016
20.5266014728990.595818315428-0.05770466867081.90247251040.2943454786123.48772791779-0.111330163314-0.1313429089090.165380515747-0.0008668702501660.07349940371450.252412530495-0.1251822909-0.5943026317140.0617647533140.2835964587360.0675080797452-0.01497965176880.3976844067920.0318549811610.4007856512846.613429641376.692440615379.7550669693
31.90734253122-0.147318098990.5320623591441.68142342774-0.1678001098541.99722245997-0.0684170991801-0.2209425222220.01662159606020.1406936363650.03420863517150.2032512175530.0122602616707-0.3333373011820.0128492842170.2358897315480.00479969003320.03712655650810.348508596667-0.002847347621020.2580572991659.2573798438259.995803767689.3823049229
42.338411914030.629328656918-0.7208578813210.865606331577-0.4417919509171.24916894534-0.1360505976890.369690645734-0.24374388759-0.1736409880060.0690190750574-0.1317090628970.259287329865-0.05546264079910.07102038605050.2890313774630.002772065174650.0007578160904340.293045879748-0.04855314316090.24197722874130.169882279553.016855478670.0151375437
50.1135298931080.3525262915770.2206290808062.27883515244-0.3852031572722.84725659181-0.207962705965-0.0123302219942-0.02433370237030.0939377310048-0.0855915557087-0.3338365860710.1454686818420.4986244950510.2790746375520.2350764056940.05583404037080.00473078271720.3465107436750.01591064690160.35377561281448.925631588459.611974428473.9346258567
61.87077875059-0.21232966398-0.2468691677541.31956264989-0.2080113561731.80980760067-0.04756101205660.113194850469-0.282499325444-0.0454480704656-0.095303363114-0.2148275374610.2619035549760.1699620503150.1244969036650.240254860420.0349049956501-0.01114926254010.3088357110630.01122118938630.33377009730243.507070886453.567600895377.0224052516
71.286208980480.32106307929-0.7152827219461.02592741478-0.1641716510920.856518002375-0.0074153526689-0.199041557607-0.157833152410.156868676991-0.106324550136-0.1336973616880.2151407442660.4129769115080.09947752848690.3808939955190.06789461933890.009475238566990.4528120900710.07292624350150.28778235932420.661067947683.840420845741.1551649299
82.707152026420.02950090133360.77299937751.26517858642-0.1989420086023.32424837906-0.109694185432-0.191308533556-0.01622164449480.2563791599110.0778386264033-0.0260932927537-0.1201820079230.2458794557810.03813647839920.3296915595420.05944906140340.0067440286980.287126527584-0.008089825264280.263919864139.4889597337894.543362894137.7722538576
91.04220135822-0.1297977231010.1336762003630.791895718634-0.1663000172590.995686585373-0.0329038195654-0.07364625292550.1298760879320.118986781897-0.0399870794639-0.0729396818801-0.1582813864140.1943365551410.05628059159850.326500961867-0.00108623562289-0.02057471358160.3641992969780.03432743675170.28314637106321.892467492596.527505022228.17838377
101.894827022690.1634290268570.06400040075513.452561912681.773285767451.36867221275-0.0283836006916-0.195413098585-0.101349742581-0.189136704490.0832018718976-0.3599901810910.07644007047040.7492939246830.01967624197740.290086899229-0.0003905152082190.01510777978740.7223201125490.05354390733330.32882597921435.414481963293.356445888333.1564364786
112.076832879940.413308254236-0.120598438761.506103724-0.3387257699011.21232171889-0.0275378060207-0.0623982264036-0.2146605615860.18803112444-0.0687800514647-0.03328719840280.3225540182880.09376505403120.08809654617840.5134882504940.09219647403930.07550382354450.2867778605660.07139030694240.29917228640910.621122841962.141798928136.2276209836
121.42253707951-0.212554264186-0.3563376750161.464805775110.07343675757312.109982928-0.0494554962857-0.0524154967788-0.2791088776280.116519288029-0.0415711047788-0.1282058069310.405377529290.2511643013060.06852587712040.4615033210420.1138387589970.05323925543760.3058568444440.04300904898870.32510816099214.911657160759.813229609628.8013772474
131.20144487144-0.3451706041120.414260434450.8660091680880.2388500721371.12990160312-0.111489706146-0.15701242299-0.07071515269640.2656036025880.01846606306020.2564532596170.227519495224-0.3825980263440.06154401253590.458785216299-0.0740096477520.129414529510.3319112167020.006744821720950.39119444096663.881290839569.696998041531.7370422341
141.86070134183-0.2244977827410.5447789351740.979319247368-0.3016288212081.192843127240.0308232212121-0.0578354267795-0.3384563484360.184768480364-0.0186054639680.2453409804450.610382430564-0.236474427971-0.05758626004710.611238065198-0.1448428528230.162763441270.347815953197-0.05338511030570.48291555623965.791949078454.862867338722.6774679148
150.8415951134230.1965126648-0.05167751006431.33306798334-0.008234992910780.916007217465-0.04517864011090.05650936220160.02704235594390.00696397909141-0.008403005557660.1712566446080.0279749159013-0.285982831740.05136821598670.2592666614050.01415317484270.04483323774610.3621004565180.02152036044990.26980581249267.292529198788.514311180821.2344268213
160.876408754232-0.0156105106722-0.2939808991232.07195441817-0.05865304221931.318620612030.09569562159030.1654088355950.467051505923-0.06187062893350.0623727258392-0.0860039444766-0.5702351125930.06784061443980.08787264205140.533348445075-0.190621594309-0.07323899123430.5105865451420.1460621199280.5108066593355.2825083662100.64237741366.9094257322
170.856646192289-0.298063529917-0.1953001215092.12208838567-0.1199956113091.82923284283-0.01948107381310.286772482610.2987631003660.0408633878576-0.0762210520170.160099838533-0.3718305700770.1057783325350.1112672286270.386994041955-0.0143724235093-0.07683875735680.3498877060970.1346078333710.39712548859844.39661133193.884139244364.2473320926
180.848750807453-0.164600353126-0.0879718918622.03937275489-0.002226451349281.798517692110.0842022325990.2288507652050.359878753162-0.168094855321-0.07599974959160.0658840297992-0.3409233883840.3391355795190.1366257882950.26344879071-0.00530868012889-0.02144755542320.4265266623160.0875808194950.33786240100148.930061148783.620026573262.3680065569
191.58011760728-0.3621642371690.6637401568712.2612891254-0.09395367037421.07229069083-0.0908445392940.2009617055480.0171228241352-0.10240265202-0.0868899702359-0.259410294146-0.05481585113880.4158368787840.09980728479290.257698853555-0.0200894211403-0.005144544940660.5367356168840.08518674215160.38832881059560.794338408176.899601219566.0120010324
201.35820542889-0.0651154940881-0.1006239678371.335066090880.01888024977681.28806115546-0.0373097843718-0.0135536823390.1603810713610.0187120952597-0.0683959150758-0.233159928676-0.1966960379130.4607035107590.04180829351190.349319167543-0.121265828394-0.06498534871320.4568335902780.1160230636750.39021317985862.441244663591.985981488277.2083451766
210.8443004408490.254504465714-0.5559697482951.403387218420.1496115703831.29445412593-0.0134084458447-0.004199941201420.736777804817-0.08359146270490.050884407102-0.395637752283-0.5071674777120.498663052850.03119993241350.512882388915-0.244160190518-0.07751050955190.537122250380.1730407739940.53532367189965.0052619688102.84553680572.7904778576
220.420964491508-0.371892397796-0.2099698381350.707425887665-0.1215821767930.573551127715-0.1846793722850.7329072905430.444307333532-0.7896013104960.08804856468160.426051425299-0.237508335691-0.04398021302480.02424283254390.5496971917020.0320144700747-0.2094712836310.365449095050.1785485095190.65127254909827.934547941699.185471901764.5215412534
231.012440382830.745232510002-0.2526861299120.9269518230650.2049719861651.08315757259-0.05701573950860.05955204778990.3276104711370.0728556204766-0.02527191527170.231760438417-0.257088785479-0.09973277778830.08913931898410.4070367479110.0597983038375-0.08708535958070.2883065495690.05350156745220.53406945201327.411833153696.706263528675.8872113875
241.69350921205-0.6227401271240.2620175055022.35172092579-0.1584479210792.50929862406-0.0633794814531-0.2653198421450.4292764824260.1985482034260.02238359943050.610812487241-0.258860035951-0.3406722083410.1453000374380.3653311489210.0528591565337-0.01393574174170.261019876745-0.04082784608640.5446197685921.234430882395.296926665484.3424530114
250.6642304083140.1940336338760.5180645359541.643059290350.3171887648661.7091714937-0.202437585145-0.05995113423690.6205758280410.0914020967974-0.02482926192570.173207705423-0.488084405514-0.1303322191760.1540831278870.4781232475960.0272402045125-0.06283316549030.2920698185890.01779427678140.53647511862829.9993523232100.17196327181.5027612171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 305 )
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 399 )
5X-RAY DIFFRACTION5chain 'A' and (resid 400 through 440 )
6X-RAY DIFFRACTION6chain 'A' and (resid 441 through 536 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 156 )
9X-RAY DIFFRACTION9chain 'B' and (resid 157 through 289 )
10X-RAY DIFFRACTION10chain 'B' and (resid 290 through 330 )
11X-RAY DIFFRACTION11chain 'B' and (resid 331 through 440 )
12X-RAY DIFFRACTION12chain 'B' and (resid 441 through 536 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 128 )
14X-RAY DIFFRACTION14chain 'C' and (resid 129 through 258 )
15X-RAY DIFFRACTION15chain 'C' and (resid 259 through 536 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 28 )
17X-RAY DIFFRACTION17chain 'D' and (resid 29 through 67 )
18X-RAY DIFFRACTION18chain 'D' and (resid 68 through 128 )
19X-RAY DIFFRACTION19chain 'D' and (resid 129 through 188 )
20X-RAY DIFFRACTION20chain 'D' and (resid 189 through 289 )
21X-RAY DIFFRACTION21chain 'D' and (resid 290 through 330 )
22X-RAY DIFFRACTION22chain 'D' and (resid 331 through 368 )
23X-RAY DIFFRACTION23chain 'D' and (resid 369 through 405 )
24X-RAY DIFFRACTION24chain 'D' and (resid 406 through 461 )
25X-RAY DIFFRACTION25chain 'D' and (resid 462 through 536 )

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