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- PDB-6ui3: GH5-4 broad specificity endoglucanase from Clostridum cellulovorans -

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Basic information

Entry
Database: PDB / ID: 6ui3
TitleGH5-4 broad specificity endoglucanase from Clostridum cellulovorans
ComponentsCellulase
KeywordsHYDROLASE / Cellulase / xylanase / GH5 / endoglucanase
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Carbohydrate binding module 65 domain 1 / Carbohydrate binding module 65 domain 1 / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat ...Carbohydrate binding module 65 domain 1 / Carbohydrate binding module 65 domain 1 / : / Clostridium cellulosome enzymes repeated domain signature. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesClostridium cellulovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: pdbx_database_related
Revision 1.2Feb 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 1.3Oct 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3423
Polymers38,2181
Non-polymers1242
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.144, 89.095, 91.083
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: 38218.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulovorans (bacteria) / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: D9SV64, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 26% PEG 3350 and 100 mM Bis-Tris pH 5.5 crystals were cryoprotected by supplementing crystallization reagent with 1.5% 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: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→31.85 Å / Num. obs: 85209 / % possible obs: 95.68 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 10.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04056 / Rpim(I) all: 0.01633 / Rrim(I) all: 0.04379 / Net I/σ(I): 29.24
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.2091 / Mean I/σ(I) obs: 7.53 / Num. unique obs: 6846 / CC1/2: 0.956 / Rpim(I) all: 0.09929 / Rrim(I) all: 0.2333 / % possible all: 78.27

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDY

3ndy


Resolution: 1.3→25.09 Å / SU ML: 0.0899 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.5237
RfactorNum. reflection% reflection
Rfree0.1422 2099 2.46 %
Rwork0.1263 --
obs0.1267 85208 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.53 Å2
Refinement stepCycle: LAST / Resolution: 1.3→25.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 8 556 3236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722894
X-RAY DIFFRACTIONf_angle_d0.98963963
X-RAY DIFFRACTIONf_chiral_restr0.0836431
X-RAY DIFFRACTIONf_plane_restr0.0073516
X-RAY DIFFRACTIONf_dihedral_angle_d11.9521079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.1639990.1594206X-RAY DIFFRACTION73.72
1.33-1.360.16481270.15175186X-RAY DIFFRACTION90.6
1.36-1.40.15361400.1455499X-RAY DIFFRACTION95.9
1.4-1.440.13431420.13675497X-RAY DIFFRACTION96.29
1.44-1.490.16351380.12815538X-RAY DIFFRACTION96.63
1.49-1.540.16181410.12365546X-RAY DIFFRACTION96.88
1.54-1.60.12771420.125615X-RAY DIFFRACTION97.16
1.6-1.680.12241300.12225604X-RAY DIFFRACTION97.52
1.68-1.760.15231530.12285649X-RAY DIFFRACTION97.79
1.76-1.870.13691430.11975679X-RAY DIFFRACTION98.1
1.87-2.020.12461450.12485704X-RAY DIFFRACTION98.4
2.02-2.220.14711400.11715733X-RAY DIFFRACTION98.71
2.22-2.540.13391500.1135788X-RAY DIFFRACTION99.08
2.54-3.20.12921510.1255865X-RAY DIFFRACTION99.44
3.2-25.090.15451580.13446000X-RAY DIFFRACTION98.01
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)
11.22747657007-0.977995743059-0.1508553131792.311850566860.2852813306970.5491217045860.002399225862950.08724519282820.019241206161-0.0683041266240.0149892211611-0.2187329623460.005547360301980.151036304034-0.005328751183490.075936163443-0.01517684877650.007536388461720.121515269755-0.001942961254730.10281335435748.465966353946.941308291322.1891921906
20.9598483670330.5916839657220.3134925291830.9429410632620.2850990733980.657232596985-0.02814846613390.08320164838920.0326445750379-0.07662719714570.0235028833196-0.00013769697876-0.07765104585580.02745502151620.006041798474510.083950399853-0.004404284042280.001837108655960.08788956252830.004973024970130.06646326050233.390601784553.425196082316.0652629047
32.290153214730.656324470691-0.4010183942450.994894399102-0.002625359310610.8461333499750.0200497950738-0.029906387608-0.03880414971260.00934975449786-0.02577349783420.04488868828880.011320342971-0.06132118070250.01026836748090.05886361393120.00573566616454-0.01180226559280.07058792292740.01030180895340.049533898467528.195856408341.231412236122.7054363563
41.1291765066-0.00796077514642-0.6144958774810.7499842830890.0777127126121.89949595069-0.0223200005751-0.00793343672855-0.03550178354740.02977341948590.0288846825677-0.001061207277550.0708609317899-0.0691456025109-0.001651116366580.0572732965286-0.00190655274876-0.008415826433320.0589050097078-0.001001140613880.063688824041533.763592744839.093095380629.6956494368
50.448798911529-0.263945164205-0.07830264073061.335162253070.3073830733080.721653632498-0.000672863840931-0.02098182637460.01647211836750.04325754682280.00333014771804-0.00392234911104-0.006388374720160.0283128616664-0.004262380056220.0544883845245-0.003264592628030.002804756874730.0701199042388-0.002189130324080.059098771018539.701315943655.976504570641.1458185686
63.12538356889-1.698412161712.210120416163.17016612917-2.421937040142.42827145307-0.0621819533054-0.1025139807830.1407475726320.08170452868460.09573328756280.0864568921801-0.0955528296508-0.0580619153649-0.04475695934560.0798834080493-0.005782158003480.01052127149050.0664862562115-0.0132836760260.05544572720435.402505456561.403708905330.680691848
71.154444806081.317470581741.146076913083.19025222436-0.9566338061824.48636218469-0.0663360199050.1585220873470.125807470118-0.0897275170829-0.0764495584084-0.088896315853-0.1013456258090.1824484409610.1381971027070.075858903117-0.005059291548730.03188051468560.0709082885171-0.007214316473480.072383161679643.699731713866.410317149128.1104839212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 216 )
5X-RAY DIFFRACTION5chain 'A' and (resid 217 through 297 )
6X-RAY DIFFRACTION6chain 'A' and (resid 298 through 315 )
7X-RAY DIFFRACTION7chain 'A' and (resid 316 through 340 )

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