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- PDB-8ghy: Crystal Structure of the E154D mutant CelD Cellulase from the Ana... -

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Basic information

Entry
Database: PDB / ID: 8ghy
TitleCrystal Structure of the E154D mutant CelD Cellulase from the Anaerobic Fungus Piromyces finnis in the complex with cellotriose.
ComponentsCellulase CelD
KeywordsHYDROLASE / Celluase / CAZymes / glycoside hydrolase (GH) family 5 / dockerin domain
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Fungal dockerin domain superfamily / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-cellotriose / Cellulase CelD
Similarity search - Component
Biological speciesPiromyces finnis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDementieve, A. / Kim, Y. / Jedrzejczak, R. / Michalska, K. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2023
Title: Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis.
Authors: Dementiev, A. / Lillington, S.P. / Jin, S. / Kim, Y. / Jedrzejczak, R. / Michalska, K. / Joachimiak, A. / O'Malley, M.A.
History
DepositionMar 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulase CelD
B: Cellulase CelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4204
Polymers83,4112
Non-polymers1,0092
Water8,809489
1
A: Cellulase CelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2102
Polymers41,7051
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulase CelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2102
Polymers41,7051
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.495, 81.007, 131.922
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 CelD


Mass: 41705.469 Da / Num. of mol.: 2 / Mutation: E154D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piromyces finnis (fungus) / Gene: BCR36DRAFT_398243 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A1Y1V643
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


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


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium acetate, 1.2 M LiCl2 and 24% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 69108 / % possible obs: 98.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 25.89 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 21.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3429 / CC1/2: 0.579 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.78 Å / SU ML: 0.2021 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2046 3395 4.92 %
Rwork0.1764 65645 -
obs0.1778 69040 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5816 0 68 489 6373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416060
X-RAY DIFFRACTIONf_angle_d0.65788231
X-RAY DIFFRACTIONf_chiral_restr0.0506863
X-RAY DIFFRACTIONf_plane_restr0.00581074
X-RAY DIFFRACTIONf_dihedral_angle_d13.89492223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.35261340.31172651X-RAY DIFFRACTION97.14
1.82-1.850.31071570.28222692X-RAY DIFFRACTION99.23
1.85-1.880.29261380.26612745X-RAY DIFFRACTION99.55
1.88-1.910.27671450.25282722X-RAY DIFFRACTION99.65
1.91-1.940.27621390.22292711X-RAY DIFFRACTION99.41
1.94-1.980.2691370.22642742X-RAY DIFFRACTION99.86
1.98-2.020.2451280.20762737X-RAY DIFFRACTION99.76
2.02-2.060.24131180.20352761X-RAY DIFFRACTION99.76
2.06-2.10.23411530.21072711X-RAY DIFFRACTION99.76
2.1-2.150.22331500.18342720X-RAY DIFFRACTION99.86
2.15-2.210.20481530.17592729X-RAY DIFFRACTION99.72
2.21-2.270.22741590.17882732X-RAY DIFFRACTION99.55
2.27-2.330.21451270.18462748X-RAY DIFFRACTION99.58
2.33-2.410.23851260.17882750X-RAY DIFFRACTION99.48
2.41-2.490.18811570.17242735X-RAY DIFFRACTION99.31
2.49-2.590.18471320.17252757X-RAY DIFFRACTION99.35
2.59-2.710.24621520.18572726X-RAY DIFFRACTION99.17
2.71-2.850.20191420.172730X-RAY DIFFRACTION98.97
2.85-3.030.20541570.17532736X-RAY DIFFRACTION98.3
3.03-3.270.20191220.17792761X-RAY DIFFRACTION98.63
3.27-3.60.19911410.16312754X-RAY DIFFRACTION98.1
3.6-4.120.18061420.14322738X-RAY DIFFRACTION97.1
4.12-5.180.14971510.14222746X-RAY DIFFRACTION96.7
5.18-33.780.18391350.17492811X-RAY DIFFRACTION93.94
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)
11.68974365750.255910292372-0.2908669580360.2269712514240.08481614386460.5821169975860.115523973281-0.2043157807840.1559203718310.0373615557104-0.012823725179-0.0140612449745-0.1100723021170.1085869457950.0002792247421230.166338828787-0.01797376114590.005626552448080.180138565939-0.01806156716980.1533628538986.331713941724.75743537721.989269566
20.481921217017-0.268772284884-0.01857870326050.2157668395810.1237982873790.1413460627850.2183508581-0.42570941950.4433040087690.03671054447930.001740118712950.113075861657-0.123468248815-0.1478908395350.07244751854310.219380555048-0.07158605869840.03983927196010.323354347327-0.09063851703870.2248201375632.2652199606629.296208482931.0167728684
31.847345404650.2839577820820.2512941029020.1071339579670.3307552286280.9299604762620.212914399321-0.360494370681-0.2145737610350.0910074841252-0.1125188794740.02358588888250.164900666689-0.1340253809290.002782926263190.224218569937-0.04038992918970.001156146357750.2283052259070.03137384850290.224204258043-4.6837454523217.957235289225.7839904828
41.141996041790.5298629385220.09872286219280.33929399736-0.2192361279910.9429243573010.1145834837720.00951654808616-0.137665188157-0.0680789224744-0.04835150302250.1647452218540.190417850006-0.2739924177821.88583078295E-50.196691822689-0.01322351314-0.001099380074350.2478358205540.02437935846730.249900075566-12.339450889116.404439131118.8407727488
50.9962042187270.104196961241-0.09347641552790.897200340710.160309126571.241659089310.07064093251160.12140852713-0.195554369952-0.02184694612020.0522307300909-0.04756302958490.1133148889860.1048899356340.002186183175250.1600284975690.0227089326696-0.05060216152530.178064688573-0.04659065561560.1765322433157.6341170044211.47576874368.58813273921
60.1360796272580.0660824821655-0.1184998056520.07604699950950.02136199283970.1651969572560.07826198108120.3150742708820.175812287016-0.1512662158340.0287056676015-0.1577308935360.05510095374240.223447298719-8.83385132073E-60.203058504078-0.02393593059930.01973859582090.334306644452-0.02280789822420.19736816201417.168651186623.22890104222.471940969
70.928736390528-0.0863897818588-0.02548337962691.267988405430.4746298059941.082204142280.03913211594140.1287512819550.0878125813668-0.2915629083340.022201884972-0.0343912787458-0.233911670537-0.2501930624890.001388460813010.3288226614980.0701219754145-0.02210210838470.224627766886-0.03603652725140.21787774482826.704056770654.76621357528.98634926595
80.4835949872390.4170828416270.04035281019580.9935676378830.2296916427921.42725605507-0.0685103227221-0.1414357753640.202313005944-0.343764180530.143033477716-0.350617425352-0.4279869518550.2047488417890.006398752625560.4511020956120.05012979026350.06368353695370.237739327648-0.06215710801650.43157541615734.099647258966.681876234415.0638816503
92.010894525080.2272537624930.2395807235511.210570071310.4301783763841.138655783680.090475246999-0.19211253818-0.1385809409890.01989334702470.0498335983866-0.2390885448280.05793034118850.1015925419640.05059171659630.2267094269020.0514462366994-0.06665344916250.166744978322-0.07705556204720.2538979910138.759477948147.532623708525.6394292361
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 77 )AA-2 - 771 - 80
22chain 'A' and (resid 78 through 99 )AA78 - 9981 - 102
33chain 'A' and (resid 100 through 168 )AA100 - 168103 - 171
44chain 'A' and (resid 169 through 223 )AA169 - 223172 - 226
55chain 'A' and (resid 224 through 335 )AA224 - 335227 - 338
66chain 'A' and (resid 336 through 359 )AA336 - 359339 - 362
77chain 'B' and (resid -2 through 139 )BC-2 - 1391 - 142
88chain 'B' and (resid 140 through 223 )BC140 - 223143 - 226
99chain 'B' and (resid 224 through 359 )BC224 - 359227 - 362

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