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- PDB-6xso: GH5-4 broad specificity endoglucanase from an uncultured bacterium -

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Basic information

Entry
Database: PDB / ID: 6xso
TitleGH5-4 broad specificity endoglucanase from an uncultured bacterium
ComponentsCellulase
KeywordsHYDROLASE / Cellulase / xylanase / GH5 / endoglucanase
Function / homology: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / (2S)-2-hydroxybutanedioic acid / DI(HYDROXYETHYL)ETHER / Cellulase
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBingman, 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
DepositionJul 15, 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: Cellulase
B: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4265
Polymers85,1632
Non-polymers2633
Water18,8801048
1
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8454
Polymers42,5821
Non-polymers2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulase


Theoretical massNumber of molelcules
Total (without water)42,5821
Polymers42,5821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.640, 91.890, 170.850
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 Cellulase


Mass: 42581.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: H2BCH8
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1048 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein 37 mg/mL in 10 mM MOPS buffer at pH 7, 50 mM NaCl was mixed with an equal volume of reservoir solution with 0.15M DL Malic acid, 20% PEG 3350. Sample was cryoprotected with reservoir ...Details: Protein 37 mg/mL in 10 mM MOPS buffer at pH 7, 50 mM NaCl was mixed with an equal volume of reservoir solution with 0.15M DL Malic acid, 20% PEG 3350. Sample was cryoprotected with reservoir supplemented to 35% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.774901 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.774901 Å / Relative weight: 1
ReflectionResolution: 1.5→36.52 Å / Num. obs: 140750 / % possible obs: 99.96 % / Redundancy: 13.6 % / Biso Wilson estimate: 21.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07386 / Rpim(I) all: 0.02085 / Rrim(I) all: 0.07679 / Net I/σ(I): 19.45
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 13918 / CC1/2: 0.746 / Rpim(I) all: 0.3862 / Rrim(I) all: 1.444 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vdh

3vdh


Resolution: 1.5→36.52 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.4751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1699 1980 1.41 %
Rwork0.1477 138731 -
obs0.148 140711 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 17 1048 6955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726171
X-RAY DIFFRACTIONf_angle_d0.9678387
X-RAY DIFFRACTIONf_chiral_restr0.079881
X-RAY DIFFRACTIONf_plane_restr0.00641096
X-RAY DIFFRACTIONf_dihedral_angle_d13.11472180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.3219990.26679835X-RAY DIFFRACTION99.92
1.54-1.580.24661980.22889732X-RAY DIFFRACTION99.94
1.58-1.630.2369990.20459830X-RAY DIFFRACTION99.97
1.63-1.680.19441980.18139772X-RAY DIFFRACTION99.97
1.68-1.740.1842990.16729862X-RAY DIFFRACTION99.95
1.74-1.810.1999990.15699835X-RAY DIFFRACTION99.96
1.81-1.890.15871980.14669799X-RAY DIFFRACTION99.94
1.89-1.990.1818990.14679945X-RAY DIFFRACTION100
1.99-2.110.18671980.1449782X-RAY DIFFRACTION99.98
2.11-2.280.1653990.13839932X-RAY DIFFRACTION100
2.28-2.510.15611980.13319893X-RAY DIFFRACTION100
2.51-2.870.1586990.140710025X-RAY DIFFRACTION100
2.87-3.610.1721400.143510078X-RAY DIFFRACTION100
3.61-36.520.15231570.141310411X-RAY DIFFRACTION99.98
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)
10.285230506354-0.00329593378781-0.01305288082651.881634163530.127691469461.32115445809-0.04105063420510.08583712449150.203284271048-0.236528161206-0.0549506754631-0.021966124796-0.459333558709-0.02658932128490.07883203778980.3393372978090.0360226191543-0.02061241359830.1817262178370.004439454000420.19829378077551.073578112333.550481871142.3764602666
20.8215833353580.139787093689-0.1154270906841.40111262210.8942742248921.93858543643-0.003211514306480.04190020845010.122039060798-0.272561116572-0.05961748475080.126099316151-0.366169131251-0.1266983103720.07671374426670.2758755018430.047873384678-0.02435377101040.166728467621-0.004888096270620.19381391473646.732981677629.263414962839.0985071676
30.4625781735080.0657204217010.01034891202051.535381815480.791436876361.55758808547-0.03591057398730.02699335675340.00693696199687-0.2174628956470.0210562024788-0.0958592321462-0.1887166064610.04619598074380.01272712898640.2401863567980.01398584232090.02661172037480.1812692698970.00135485451550.18992978194255.961496735816.824758309532.1806311662
41.01944006650.11765884487-0.1377422556851.184489103490.2048301264431.413013881590.00222598394284-0.126306756343-0.08565577215910.0918796798909-0.0377752691607-0.006294304123780.0327718141771-0.07105719994730.0399187359460.1804741678920.0088555772234-0.01428544789860.1834107387970.00116852801310.17076376052248.427374265413.737603680653.4240542034
51.05491320967-0.2511506308880.4018788372340.8150149085280.1524007867361.438323473160.03720343506880.1296311416350.0557133723637-0.000418189073163-0.0916890038277-0.3964682027260.1173791978340.5197450133220.01581083473130.1569620904580.0365296344824-0.01117030240370.33045002270.05674523408690.29674407169754.045454064251.98096729414.24754998648
61.09638007308-0.1865819471860.5116290499891.00797542733-0.7820121719123.59189955379-0.0331318572077-0.06202227210510.1335453801710.0631678730895-0.0672229670183-0.129377326576-0.2183974110440.2288507816520.11052199840.171244164887-0.0146718149859-0.03030964290820.1726936069930.00550123213190.21866102046643.544575079763.41373814550.738000439814
71.265352581180.5979040052590.381359467651.110632984140.1650129615231.24254881402-0.02982098561640.02339935596210.0314261298384-0.0766012121488-0.0295714765777-0.04009451650920.05564011029760.05144443819460.0570250175150.1857169030380.02446440704920.006296573855750.1734189527930.002088017701030.18466140917637.739392795348.5316389823-8.4519315048
88.682137636711.029249853110.4129491436072.151010983270.5230273956172.569881573740.002992839789590.0788367116812-0.4267995206280.0185474244856-0.0300512955774-0.02787296034550.382395075001-0.1122929976660.06526975677610.258274780027-0.00482974346537-0.004196520035120.1140054047480.02486126074680.17099957299632.630962899736.0477100152-3.13554944919
90.853941131823-0.00128638806901-0.1972100730891.06969968961-0.2740837807111.56338017375-0.0143693284731-0.204174311343-0.06620120473790.1437390319850.01852119995780.07506033843560.0882932723932-0.0925322085811-0.002131083993310.1985928674170.00227074037032-0.007291381714190.2650278183180.02071169661010.21315761524131.832192474447.710070292713.601594006
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 64 )AA7 - 641 - 58
22chain 'A' and (resid 65 through 139 )AA65 - 13959 - 134
33chain 'A' and (resid 140 through 263 )AA140 - 263135 - 261
44chain 'A' and (resid 264 through 379 )AA264 - 379262 - 379
55chain 'B' and (resid 5 through 44 )BE5 - 441 - 38
66chain 'B' and (resid 45 through 113 )BE45 - 11339 - 108
77chain 'B' and (resid 114 through 236 )BE114 - 236109 - 233
88chain 'B' and (resid 237 through 263 )BE237 - 263234 - 260
99chain 'B' and (resid 264 through 378 )BE264 - 378261 - 378

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