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- PDB-6xrk: GH5-4 broad specificity endoglucanase from an uncultured bovine r... -

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Basic information

Entry
Database: PDB / ID: 6xrk
TitleGH5-4 broad specificity endoglucanase from an uncultured bovine rumen ciliate
ComponentsGlycoside hydrolase type 1
KeywordsHYDROLASE / Cellulase / xylanase / GH5 / endoglucanase
Function / homologyorganic substance metabolic process / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / DI(HYDROXYETHYL)ETHER / Glycoside hydrolase type 1
Function and homology information
Biological speciesuncultured bovine rumen ciliate (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.419 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 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 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: Glycoside hydrolase type 1
B: Glycoside hydrolase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,42510
Polymers85,7682
Non-polymers6578
Water18,5371029
1
A: Glycoside hydrolase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1534
Polymers42,8841
Non-polymers2693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2726
Polymers42,8841
Non-polymers3885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.320, 84.990, 121.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase type 1


Mass: 42883.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: uncultured ciliate from bovine rumen
Source: (gene. exp.) uncultured bovine rumen ciliate (environmental samples)
Plasmid: pVP67K
Details (production host): Expression plasmid developed at the Center for Eukaryotic Structural Genomics
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3) / References: UniProt: G5DDB8, Hydrolases

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Non-polymers , 5 types, 1037 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 1029 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 nL 37 mg/mL protein, 50 mM sodium chloride, 10 mM MOPS, pH 7 + 200 nL reservoir solution (200 mM ammonium acetate, 100 mM Bis-Tris methane, pH 6.5, 25% PEG3350), MRC SD2 plate, ...Details: 200 nL 37 mg/mL protein, 50 mM sodium chloride, 10 mM MOPS, pH 7 + 200 nL reservoir solution (200 mM ammonium acetate, 100 mM Bis-Tris methane, pH 6.5, 25% PEG3350), MRC SD2 plate, cryoprotectant: reservoir solution + 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
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.774901 Å / Relative weight: 1
ReflectionResolution: 1.419→36.64 Å / Num. obs: 141292 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.07724 / Net I/σ(I): 18.36
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.415 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 13953 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JEP

2jep


Resolution: 1.419→36.64 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.98
RfactorNum. reflection% reflection
Rfree0.167 1997 1.41 %
Rwork0.145 --
obs0.145 141196 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.419→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5723 0 40 1029 6792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076044
X-RAY DIFFRACTIONf_angle_d0.9548231
X-RAY DIFFRACTIONf_dihedral_angle_d13.0742166
X-RAY DIFFRACTIONf_chiral_restr0.078889
X-RAY DIFFRACTIONf_plane_restr0.0061055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.419-1.45540.36171410.34959779X-RAY DIFFRACTION100
1.4554-1.49480.28541400.25859850X-RAY DIFFRACTION100
1.4948-1.53880.2081410.21099860X-RAY DIFFRACTION100
1.5388-1.58840.21621420.18299827X-RAY DIFFRACTION100
1.5884-1.64520.18731420.16959895X-RAY DIFFRACTION100
1.6452-1.71110.17831420.15999861X-RAY DIFFRACTION100
1.7111-1.7890.18521410.15529882X-RAY DIFFRACTION100
1.789-1.88330.181420.14469893X-RAY DIFFRACTION100
1.8833-2.00130.23171430.14419901X-RAY DIFFRACTION100
2.0013-2.15580.16431420.13669946X-RAY DIFFRACTION100
2.1558-2.37270.15241450.13099982X-RAY DIFFRACTION100
2.3727-2.71590.1441430.129910010X-RAY DIFFRACTION100
2.7159-3.42140.13581430.135210104X-RAY DIFFRACTION100
3.4214-36.640.15981500.134910409X-RAY DIFFRACTION100
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)
11.3547-0.14960.14521.1141-0.04150.81820.03150.23980.0593-0.1379-0.0691-0.06580.04140.1111-0.00080.16040.01610.01410.20120.02340.115638.843456.915437.7355
21.1922-0.43620.44230.7694-0.1090.6307-0.1034-0.07750.26010.11430.0112-0.1911-0.06280.1022-0.00220.1549-0.0229-0.02090.1744-0.01930.199448.475463.968856.9853
31.1721-0.31240.21570.9429-0.13930.9144-0.039-0.170.19040.19020.01410.0624-0.1095-0.0679-0.00050.16460.0060.01340.1728-0.02260.155532.655264.413755.4517
40.72490.31760.10440.375-0.26830.73670.0252-0.00380.01430.0380.0279-0.1442-0.00590.04400.11190.0039-0.00580.11680.00050.139473.269929.832338.1801
50.47890.26290.07241.36210.35420.8460.05110.0450.1079-0.0313-0.0079-0.2754-0.05870.03640.00040.1405-0.00040.01310.1322-0.010.195474.38337.777937.9198
60.52640.2290.46131.27020.16890.77350.00010.03080.1059-0.1064-0.01540.0009-0.0638-0.08800.16530.01560.00130.1472-0.00830.128462.055633.370632.2064
70.78340.12360.62760.91960.2940.54440.02040.0412-0.0244-0.0934-0.05590.03690.0436-0.0748-00.16820.00870.00250.1654-0.02420.132860.320427.068731.179
80.75230.09550.17010.6969-0.20130.22610.0408-0.1631-0.01250.2453-0.13190.06730.125-0.17950.00150.2149-0.04150.0030.2088-0.02080.142458.030527.163550.5567
90.16370.012-0.00470.1013-0.0390.015-0.0049-0.2577-0.17720.4323-0.14540.12290.3555-0.312-0.01640.4077-0.06790.00610.24810.04250.232162.313714.608654.66
100.978-0.254-0.40530.647-0.12170.48120.051-0.1833-0.12660.348-0.0269-0.1870.21710.03070.00080.2603-0.0082-0.05610.16020.00640.171971.102621.434449.9406
110.23140.1237-0.11520.09350.05320.5470.0469-0.0811-0.0940.38430.0713-0.44880.28240.1607-0.01490.25610.0339-0.14110.1999-0.02670.309682.567524.532852.467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 200 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 201 THROUGH 273 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 274 THROUGH 357 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 34 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 35 THROUGH 119 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 120 THROUGH 161 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 162 THROUGH 200 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 201 THROUGH 247 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 248 THROUGH 273 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 274 THROUGH 328 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 329 THROUGH 357 )

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