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- PDB-6wqv: GH5-4 broad specificity endoglucanase from Ruminococcus champanel... -

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Basic information

Entry
Database: PDB / ID: 6wqv
TitleGH5-4 broad specificity endoglucanase from Ruminococcus champanellensis with bound cellotriose
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / Cellulase / xylanase / GH5 / endoglucanase
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-cellotriose / NITRATE ION / Endoglucanase
Similarity search - Component
Biological speciesRuminococcus champanellensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Smith, R.W. / Glasgow, E.M. / Fox, B.G.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DEFC0207ER64494 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH 5 T32 GM008349 Biotechnology Training Program United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis.
Authors: Glasgow, E.M. / Kemna, E.I. / Bingman, C.A. / Ing, N. / Deng, K. / Bianchetti, C.M. / Takasuka, T.E. / Northen, T.R. / Fox, B.G.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,61713
Polymers159,2894
Non-polymers2,3289
Water26,1761453
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3893
Polymers39,8221
Non-polymers5672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4514
Polymers39,8221
Non-polymers6293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4514
Polymers39,8221
Non-polymers6283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3272
Polymers39,8221
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.610, 83.170, 85.210
Angle α, β, γ (deg.)93.982, 93.359, 89.274
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Endoglucanase / Cellulase


Mass: 39822.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus champanellensis (bacteria)
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D4LAX7
#2: Polysaccharide
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1453 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, BisTris Propane pH 7.0 and 200 mM Sodium Nitrate, 1 mM cellotriose, cryoprotected in above supplemented with 15% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2014
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→36.89 Å / Num. obs: 224235 / % possible obs: 93.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.41 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0463 / Rpim(I) all: 0.02554 / Rrim(I) all: 0.05299 / Net I/σ(I): 17
Reflection shellResolution: 1.45→1.502 Å / Rmerge(I) obs: 0.4333 / Mean I/σ(I) obs: 2.79 / Num. unique obs: 16603 / CC1/2: 0.872 / CC star: 0.965 / Rpim(I) all: 0.2622 / Rrim(I) all: 0.5093 / % possible all: 68.84

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WQP

6wqp


Resolution: 1.45→36.89 Å / SU ML: 0.1038 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.0453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.169 2075 0.93 %
Rwork0.151 222126 -
obs0.1512 224201 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10944 0 156 1453 12553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004611637
X-RAY DIFFRACTIONf_angle_d0.818515956
X-RAY DIFFRACTIONf_chiral_restr0.06681788
X-RAY DIFFRACTIONf_plane_restr0.00482074
X-RAY DIFFRACTIONf_dihedral_angle_d13.31394106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.24511040.223510239X-RAY DIFFRACTION64.55
1.48-1.520.22791190.205913406X-RAY DIFFRACTION84.37
1.52-1.560.21951310.191214988X-RAY DIFFRACTION94.18
1.56-1.610.22971380.178415107X-RAY DIFFRACTION94.69
1.61-1.660.19471410.168615087X-RAY DIFFRACTION95.1
1.66-1.720.18361450.169415141X-RAY DIFFRACTION95.42
1.72-1.790.18741400.164115197X-RAY DIFFRACTION95.75
1.79-1.870.19381340.157815262X-RAY DIFFRACTION95.97
1.87-1.970.17071550.157715276X-RAY DIFFRACTION96.27
1.97-2.090.18691520.154215344X-RAY DIFFRACTION96.52
2.09-2.250.15061440.144915454X-RAY DIFFRACTION96.94
2.25-2.480.18321310.141415435X-RAY DIFFRACTION97.22
2.48-2.840.14361120.147715488X-RAY DIFFRACTION97.46
2.84-3.570.16162140.14715399X-RAY DIFFRACTION97.28
3.57-36.890.14281150.134815303X-RAY DIFFRACTION96.15
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)
11.34776047362-0.05463409794370.3260905583041.19181571243-0.3433119101731.19065610850.001893672960920.05138448148560.0549437599217-0.045540524092-0.0375545813936-0.0644790661873-0.05225974690910.07348500280990.03585171119560.0965732398458-0.02926679460070.01338610201520.0846903069625-0.007985340190260.0799139555888-2.1552091098-15.977955473-20.0127260375
20.8072762892820.0747517469493-0.1967360658980.449413992184-0.2694909793131.419874807790.01390401887490.1008216709250.0359162365844-0.0236008289776-0.0182361787210.0817881165045-0.0433404683124-0.123464965166-0.0001987529493450.0995200742288-0.0232910765211-0.005256913974380.0846102611083-0.009663750420710.106091991699-14.380455175-16.6029447183-26.7331588322
31.731933722280.227257531201-0.2742865370191.51343464043-0.02788536136131.739889261060.0200443830324-0.0320792725479-0.07077397586460.02169685295430.0236047063220.1574926942470.0762545098951-0.128178659744-0.02095722180150.0788894413748-0.02298281548180.00153689116470.077441687970.01082634843030.112702281058-20.0641369002-24.9457472583-10.4605744082
43.10199844974-1.35921430090.2021974339242.80439972129-0.0981479752913.638757184850.00508685034512-0.25112248434-0.1600311794060.208050235523-0.0688081943250.1132795363410.176808758778-0.07799009145670.0521106754420.107763619397-0.02857417038760.01553875547640.1171759097310.01093483984760.0693392860056-7.75677511742-24.9446519418-1.69459406299
51.66160223719-0.574984141160.6865630216212.22481388815-0.2146477291341.20883731877-0.0154022884536-0.0156138079941-0.01878241577210.05442310515450.0130384515390.002859849536150.11234680808-0.002752315497660.006854477215920.09776490164820.001304678273960.03254179914710.1225632669370.0165932293520.04379992750549.6751961883-21.9597972924-55.7965930972
60.767913642036-0.0425396158022-0.08208053748570.548994824380.1308233712471.86603067916-0.0352839401747-0.0146868359746-0.05325235317420.01303505979480.02839049422360.01144064568160.1133099913890.02632431855960.01024048553950.08929540421470.0039604629550.008266636425740.099738979563-0.003453238137370.10310453460410.2366886942-23.462013678-63.2670230102
71.299107295660.7383646963171.146925383181.735899795571.038063219062.13857580141-0.06515946713770.1673795828450.0296223412419-0.07204643721990.0645994224647-0.0845204097763-0.08204767553380.228760256002-0.01245105160630.09121562427970.007501964919740.02082806444980.1481558168670.02175303302770.09830403326613.6966200013-8.45645544531-64.5174685666
82.29860185578-0.3745595583770.5979787962372.47709246196-0.2858612409741.91174769215-0.0019229278635-0.04176418107750.170106727898-0.0192326930366-0.0314870190157-0.0738556930035-0.1549542474050.1302638031280.04362732104280.0871801821393-0.01032459431230.0264838714760.11541504211-0.009556529564130.09834658924715.137070489-2.98727487854-57.3455415778
93.003747201090.629570460314-0.3754053897884.59878316312-1.083858294094.37834252464-0.0761420608489-0.2634408518280.2554644699490.3878476094190.103439655911-0.131859006171-0.2028189299450.143950637909-0.001807471977950.08670533070260.00497352151958-0.01842212836260.186116415029-0.03526714464160.09266297472517.253666633-8.97013700375-43.5769412923
100.185127276443-0.3921891956070.1247144014341.22342159430.156774335950.8084124279780.0534042701422-0.015955868525-0.124149807084-0.124143887096-0.0460889975906-0.02021032676650.2757679408950.06977704926790.03265447283660.224909028495-0.056662231149-0.01257748037160.140518541175-0.009588711058990.18251753654819.3180920775-65.1975945136-11.5265586353
116.996658930362.80516675925-2.577649106655.00872292712-0.5767498366934.20877998043-0.1115666598420.627009321709-0.37807868659-0.4318415333910.214490337111-0.02097023591240.4146580630760.0601193563802-0.08972635287460.283530845323-0.0094391934467-0.05152854794530.208622671846-0.0583041175910.17491083433516.0666130508-65.2529660862-22.8507063448
121.306913405920.150565190977-0.02574203004511.64408827563-0.4791610271561.663321668080.166263328338-0.0894181855719-0.4335934228470.014270590585-0.0115254987058-0.02676348699180.4985190246310.0949672308439-0.07930599817980.284443282674-0.0507484083648-0.04968324401020.1366118311920.001665989393640.26268737950118.8072732022-70.0949523927-7.76223423828
133.36869128730.241203271575-0.5777071437132.30219234189-0.2063406829142.629373423720.264603089277-0.339215367209-0.5805625435740.307197417703-0.0728133985824-0.157298816350.575333901282-0.0352933345451-0.1356285715920.401798928068-0.0528046494379-0.1127848858330.1773369747780.07206045397510.34552222979521.7732084967-73.59827392072.83659642446
142.842485657210.554094385882-0.5970722423052.581597187740.293267392823.859291104320.0711828734604-0.122404902827-0.1905732743410.205166543236-0.124163901410.1219175366520.214492779893-0.2620002662230.05315834469630.177223640006-0.0559470045742-0.04138821007470.149421152992-0.001218625895030.17022868027917.7928874717-61.5035702586-1.27720244915
151.63987971018-0.2417842445850.8224191505872.14459581156-0.6678354601191.674901833420.0450767231671-0.222504709362-0.04218892250620.1570971197740.0132561195956-0.05082254044050.129401014281-0.0489247819947-0.06161115959450.146865835656-0.0463659015272-0.01174956723830.136465862337-0.008699486137380.14269500377320.730627891-56.44945766710.960458937512
161.591057075-0.03290676937360.2198797249161.69403773097-0.005882092079151.3718461155-0.05121501228580.02596351700620.146151860101-0.08684426278720.05364578586460.11335148416-0.0224812382313-0.05666323131040.02328672558370.134479437135-0.0519161563573-0.02785310299040.1065103206560.0243123429160.18007622978716.3598305088-45.8109871188-10.7027700573
173.65218357659-2.29437970508-1.728779834853.77320948116-0.03001259995114.550204120360.02827165605990.572159535070.200485286212-0.61139464803-0.15563234239-0.0030382044184-0.1878845170680.1199182551310.1125653878790.254850441116-0.0502143585988-0.04213325782110.2539871819180.04801522645740.14341493966114.4573338028-52.2254318718-24.5869017127
181.39577204041-0.9092933755510.1019100034960.963469770027-0.0463989244030.628119695661-0.331489523611-0.391512140944-0.2514290544740.4562598283410.2426821805620.226663180936-0.147115804029-0.2273443704080.08246208025550.3728099027820.1812838540870.01245399784770.3099372129190.04744544150250.27945795885-14.3280724804-57.78194626-49.4655464923
193.222403902451.423827627840.5357554893795.243953287230.7641781295431.70804744946-0.07526940102740.0174008789107-0.318602124765-0.1114094570070.1356390245520.432541480612-0.169100893428-0.287706365884-0.05723593634760.2730627641350.0910822278643-0.06232666703620.2489803012510.02072765325960.345442891404-20.0166434168-58.5476692212-59.8246070275
200.60377327581-0.2958862546740.2326348612390.9439515596650.1980228804520.925320007353-0.23979945025-0.53359500042-0.1407076549490.4137634289270.2612732623820.184845231982-0.234630012448-0.4027432167570.2601325823660.4744960879360.3239314807410.03084517459290.4280698955660.01688484801930.28692387618-15.8002994064-53.7850035199-45.039029064
210.50325502884-0.484699069049-0.08880579417560.9158011319490.1330983007330.166043431106-0.0787669534954-0.108645120540.0293412988220.1330187317960.08663512465570.0160706052185-0.0424985683683-0.03096165785790.02527958453850.6644018208910.4267925055460.007940481550720.6361299560680.009382936240760.248542655481-13.5029862864-51.2331218446-34.0192764045
222.024603791790.271129658120.3330200564691.420876302110.1094851946380.836748477215-0.399965183984-0.4152880262560.08804245209970.3170558459250.3303329452050.0923782007438-0.254243380366-0.1861947961260.05779598178950.4938523337990.259048076411-0.03686501689230.391680135090.01181348566540.235825679683-5.35146588267-55.2930921756-43.5716362601
230.208085290608-0.2437744054450.3030895973831.109665605480.2429463618270.876720281766-0.309568490024-0.4225801402630.02776560534570.4661413945170.355505895771-0.00458091230788-0.0639795889635-0.1518441729210.02685967653820.589441944270.343886769977-0.0478451988990.496347413119-0.04884284354860.227492747583-3.12153684833-58.5445298695-36.6222309908
241.50530298188-0.279230294306-0.2620033765161.177057943930.6003444486932.44702672744-0.259683096413-0.3005383510590.1360591468820.1525505841980.181984800777-0.20334988213-0.1706316883790.06576135730490.04523392659490.3316617559310.1480051723430.0002671047890040.2587782828740.01823482887530.2825034845391.70433855174-61.0145335802-50.042209121
252.35005671252-0.150773701891-1.020429384111.726678527540.120348018763.90763619075-0.150971638415-0.1460191045120.1114581936810.1651681782820.176591576843-0.377766428844-0.09641524728520.207036386399-0.02728601360150.2750668155250.0589174492255-0.03009166469590.151373945416-0.03618007572250.2462649567555.61041683141-65.8099663436-54.6698879819
263.31880726089-1.228659728391.633636026185.85603580915-4.436891880917.491110580270.184386892170.335030085040.0438273835363-0.502604953605-0.06567706294610.01913820571510.0938875464225-0.0754537119185-0.1058892395240.2036404779790.05949967936830.02100985862230.125896623421-0.01309641986580.1723909674432.03460382822-69.6409370087-62.2750722395
272.98317852306-0.4260225879081.173722716131.49945362775-0.4226865820653.484438992410.08168084456370.220154247878-0.19466173701-0.535971323006-0.05544558286040.1968113377150.123188164091-0.0932558502425-0.001866074490590.3061357206360.0684514179581-0.01434276486950.17232867052-0.02332689566170.215299539439-8.79601158165-61.6963934738-64.0448118572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 131 )
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 259 )
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 332 )
4X-RAY DIFFRACTION4chain 'A' and (resid 333 through 354 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 50 )
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 223 )
7X-RAY DIFFRACTION7chain 'B' and (resid 224 through 259 )
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 332 )
9X-RAY DIFFRACTION9chain 'B' and (resid 333 through 354 )
10X-RAY DIFFRACTION10chain 'C' and (resid 11 through 50 )
11X-RAY DIFFRACTION11chain 'C' and (resid 51 through 68 )
12X-RAY DIFFRACTION12chain 'C' and (resid 69 through 131 )
13X-RAY DIFFRACTION13chain 'C' and (resid 132 through 149 )
14X-RAY DIFFRACTION14chain 'C' and (resid 150 through 178 )
15X-RAY DIFFRACTION15chain 'C' and (resid 179 through 259 )
16X-RAY DIFFRACTION16chain 'C' and (resid 260 through 332 )
17X-RAY DIFFRACTION17chain 'C' and (resid 333 through 354 )
18X-RAY DIFFRACTION18chain 'D' and (resid 11 through 50 )
19X-RAY DIFFRACTION19chain 'D' and (resid 51 through 68 )
20X-RAY DIFFRACTION20chain 'D' and (resid 69 through 131 )
21X-RAY DIFFRACTION21chain 'D' and (resid 132 through 149 )
22X-RAY DIFFRACTION22chain 'D' and (resid 150 through 178 )
23X-RAY DIFFRACTION23chain 'D' and (resid 179 through 223 )
24X-RAY DIFFRACTION24chain 'D' and (resid 224 through 259 )
25X-RAY DIFFRACTION25chain 'D' and (resid 260 through 296 )
26X-RAY DIFFRACTION26chain 'D' and (resid 297 through 314 )
27X-RAY DIFFRACTION27chain 'D' and (resid 315 through 354 )

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