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- PDB-6q1i: GH5-4 broad specificity endoglucanase from Clostrdium longisporum -

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Basic information

Entry
Database: PDB / ID: 6q1i
TitleGH5-4 broad specificity endoglucanase from Clostrdium longisporum
ComponentsEndoglucanase A
KeywordsHYDROLASE / GH5-4 / endoglucanase / GLBRC
Function / homology
Function and homology information


cellulase / beta-glucosidase activity / polysaccharide binding / cellulase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / : / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 ...Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / : / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesClostridium longisporum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBianchetti, C.M. / Bingman, C.A. / Fox, B.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-07ER64494 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
DepositionAug 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Structure summary / Category: pdbx_database_related / struct / Item: _struct.title
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

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Assembly

Deposited unit
A: Endoglucanase A
B: Endoglucanase A


Theoretical massNumber of molelcules
Total (without water)80,1112
Polymers80,1112
Non-polymers00
Water14,826823
1
A: Endoglucanase A


Theoretical massNumber of molelcules
Total (without water)40,0551
Polymers40,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase A


Theoretical massNumber of molelcules
Total (without water)40,0551
Polymers40,0551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.350, 53.480, 68.060
Angle α, β, γ (deg.)104.048, 96.886, 87.065
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 A / Cellulase A / Endo-1 / 4-beta-glucanase A


Mass: 40055.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium longisporum (bacteria) / Gene: celA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P54937, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystals were set with a Mosquito into SD2 plates. The condition that provided the crystals for this data set came from Morpheus Screen D9: 10% Alcohols, 50% Tris/Bicine H 8.5, and 15% P550MME_P20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.35→25.21 Å / Num. obs: 128382 / % possible obs: 94.83 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04018 / Rpim(I) all: 0.02412 / Rrim(I) all: 0.04695 / Net I/σ(I): 20.86
Reflection shellResolution: 1.35→1.398 Å / Rmerge(I) obs: 0.1076 / Mean I/σ(I) obs: 8.28 / Num. unique obs: 12528 / CC1/2: 0.988 / Rpim(I) all: 0.07146 / Rrim(I) all: 0.13

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Processing

Software
NameVersionClassification
XDS20190315data reduction
XSCALE20190315data scaling
PHASERphasing
PHENIX1.15.2_3472refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDY

3ndy


Resolution: 1.35→25.21 Å / SU ML: 0.0975 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 13.5275
RfactorNum. reflection% reflectionSelection details
Rfree0.1317 1980 1.54 %thin shells
Rwork0.1116 ---
obs0.1119 128313 94.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.77 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5525 0 0 823 6348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515889
X-RAY DIFFRACTIONf_angle_d0.84978073
X-RAY DIFFRACTIONf_chiral_restr0.0757887
X-RAY DIFFRACTIONf_plane_restr0.00581041
X-RAY DIFFRACTIONf_dihedral_angle_d12.14542173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.2093990.13168829X-RAY DIFFRACTION92.47
1.38-1.420.13761980.10378841X-RAY DIFFRACTION93.25
1.42-1.460.1257990.08878909X-RAY DIFFRACTION93.54
1.46-1.510.13211980.08368891X-RAY DIFFRACTION94
1.51-1.560.1116990.0869050X-RAY DIFFRACTION94.32
1.56-1.630.1248990.0869079X-RAY DIFFRACTION94.79
1.63-1.70.12191980.09048925X-RAY DIFFRACTION95.24
1.7-1.790.1207990.0929173X-RAY DIFFRACTION95.5
1.79-1.90.11081980.09829074X-RAY DIFFRACTION95.95
1.9-2.050.1335990.09899209X-RAY DIFFRACTION96.28
2.05-2.260.10741980.09769110X-RAY DIFFRACTION96.38
2.26-2.580.1143990.10899250X-RAY DIFFRACTION96.99
2.58-3.250.14331980.12549231X-RAY DIFFRACTION97.18
3.25-25.210.163990.15128762X-RAY DIFFRACTION91.9

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