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- PDB-8ghx: Crystal Structure of CelD Cellulase from the Anaerobic Fungus Pir... -

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Basic information

Entry
Database: PDB / ID: 8ghx
TitleCrystal Structure of CelD Cellulase from the Anaerobic Fungus Piromyces finnis
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
Biological speciesPiromyces finnis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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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)84,14812
Polymers83,5272
Non-polymers62110
Water1,69394
1
A: Cellulase CelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1988
Polymers41,7641
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulase CelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9504
Polymers41,7641
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.726, 81.850, 133.259
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: 41763.504 Da / Num. of mol.: 2
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 0.1 M Tris-HCl buffer, pH 8.7, 0.5 M LiCl2 and 28% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 28052 / % possible obs: 99.2 % / Redundancy: 10.6 % / Biso Wilson estimate: 35.24 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.74 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1348 / % possible all: 98.3

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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: 2.46→48.17 Å / SU ML: 0.232 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 1388 4.96 %
Rwork0.1881 26587 -
obs0.1902 27975 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.31 Å2
Refinement stepCycle: LAST / Resolution: 2.46→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 40 94 5888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185965
X-RAY DIFFRACTIONf_angle_d0.41288071
X-RAY DIFFRACTIONf_chiral_restr0.0419821
X-RAY DIFFRACTIONf_plane_restr0.00361068
X-RAY DIFFRACTIONf_dihedral_angle_d12.62412154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.550.28231290.23482428X-RAY DIFFRACTION91.45
2.55-2.650.28941190.24362653X-RAY DIFFRACTION99.46
2.65-2.770.27971380.22682652X-RAY DIFFRACTION99.57
2.77-2.920.23861350.21072658X-RAY DIFFRACTION99.4
2.92-3.10.25471480.20832609X-RAY DIFFRACTION99.1
3.1-3.340.23711330.20312683X-RAY DIFFRACTION99.51
3.34-3.670.22521450.18062691X-RAY DIFFRACTION99.86
3.68-4.210.20431400.1642647X-RAY DIFFRACTION98.52
4.21-5.30.18811490.15772734X-RAY DIFFRACTION99.86
5.3-48.170.2381520.18192832X-RAY DIFFRACTION98.64
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)
12.159761426440.172160319640.3393262898621.564074117450.1748155733112.38598168060.0838694335121-0.470747707243-0.1541363006860.2239464152270.03077705692910.07642128814250.267898960365-0.0112728582534-0.1128475449750.199515850002-0.00561299616645-0.004292348213350.2963574671630.02590857935640.194392797525-5.30741061881-25.955178635624.1581577023
23.85259523311.671222863281.056674968023.589503079810.2206774060373.873018442980.0755074432245-0.301245917290.3785913099310.234773474131-0.0395589674839-0.059040020177-0.4525890217270.234332573127-0.03124440845290.2412209711090.02537638357340.01549847434710.318240848491-0.024776727610.2366924831668.15699320087-17.448604356422.8356195528
32.792821534860.318363607710.1489305189552.33293744489-0.09418571802942.169103783810.06226342913960.1750927016170.3641557163570.01811803569350.02693116534790.141484797203-0.189055646167-0.170515965731-0.08559324157250.1871756487040.0367157299740.02564793208160.2586530735980.05135069765050.20054265174-9.40057681077-13.32964503117.60560219796
41.867669560770.277654897123-0.02786792669081.54912778684-0.1096486512462.892168812970.07656493369020.257983347088-0.0319468976474-0.377856728983-0.013614953221-0.1551790474750.1961527971660.443965131112-0.07080537652470.3378251076910.08370973558150.05202468553890.2942039020610.04585842132020.299551291654-25.3270379524-51.884249130710.6747738104
53.521540793921.80992463704-0.4504323954644.169721444010.3688014262684.16842056159-0.1072201825410.345691266674-0.425283969386-0.5052994818570.08524559540320.5088289208260.606416782235-0.4538102926630.005601996714680.5215823631790.0763850757818-0.04958258211390.356008070027-0.0041589304280.464905592175-33.0427430151-66.200145976712.4659743664
63.889781488050.487044835758-0.3045986350091.73546273382-0.7734575095042.803745424140.238643323368-0.2539375418610.3693720564430.0645806053510.03618908254370.362377694239-0.193233092656-0.260880830441-0.223437233940.3121063377480.05906316436040.1034261446340.2270163376520.04260868345120.32257231411-39.5767392961-48.383498488325.8814144461
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 99 )AA-1 - 991 - 101
22chain 'A' and (resid 100 through 223 )AA100 - 223102 - 225
33chain 'A' and (resid 224 through 360 )AA224 - 360226 - 362
44chain 'B' and (resid -2 through 101 )BI-2 - 1011 - 104
55chain 'B' and (resid 102 through 223 )BI102 - 223105 - 221
66chain 'B' and (resid 224 through 357 )BI224 - 357222 - 355

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