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- PDB-5wh8: Cellulase Cel5C_n -

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Basic information

Entry
Database: PDB / ID: 5wh8
TitleCellulase Cel5C_n
ComponentsPutative carbohydrate-active enzyme
KeywordsHYDROLASE / cellulase / GH5
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Putative carbohydrate-active enzyme
Similarity search - Component
Biological speciesuncultured organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsKoropatkin, N.M. / Pope, P.B. / Naas, A.E.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway214042 Norway
European Research Commission Starting Grant Fellowship336355 - MicroDE Norway
CitationJournal: Microbiome / Year: 2018
Title: "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.
Authors: Naas, A.E. / Solden, L.M. / Norbeck, A.D. / Brewer, H. / Hagen, L.H. / Heggenes, I.M. / McHardy, A.C. / Mackie, R.I. / Pasa-Tolic, L. / Arntzen, M.O. / Eijsink, V.G.H. / Koropatkin, N.M. / ...Authors: Naas, A.E. / Solden, L.M. / Norbeck, A.D. / Brewer, H. / Hagen, L.H. / Heggenes, I.M. / McHardy, A.C. / Mackie, R.I. / Pasa-Tolic, L. / Arntzen, M.O. / Eijsink, V.G.H. / Koropatkin, N.M. / Hess, M. / Wrighton, K.C. / Pope, P.B.
History
DepositionJul 15, 2017Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.2Jan 17, 2024Group: 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: Putative carbohydrate-active enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,10717
Polymers36,6291
Non-polymers1,47916
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint41 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.210, 75.500, 88.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative carbohydrate-active enzyme


Mass: 36628.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured organism (environmental samples)
Gene: SARM_0026 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9NSK2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.09M NaF, 0.09M NaBr, 0.09 M NaI, 0.1 M imidazole, MES monohydrate pH 6.5, 20% PEG 500 MME, 20% PEG 20K

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Data collection

DiffractionMean temperature: 150 K / Ambient temp details: liquid nitrogen vapor
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.57→27.57 Å / Num. obs: 46380 / % possible obs: 98.76 % / Redundancy: 5.9 % / Biso Wilson estimate: 13.82 Å2 / Rmerge(I) obs: 0.06999 / Net I/σ(I): 19.1
Reflection shellResolution: 1.57→1.626 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.8158 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 4564 / CC1/2: 0.854 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZT

3pzt


Resolution: 1.57→27.566 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 16.94
RfactorNum. reflection% reflection
Rfree0.174 2000 4.31 %
Rwork0.1448 --
obs0.146 46374 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.38 Å2 / Biso mean: 17.6653 Å2 / Biso min: 6.38 Å2
Refinement stepCycle: final / Resolution: 1.57→27.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 231 219 3030
Biso mean--35.16 26.79 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012770
X-RAY DIFFRACTIONf_angle_d1.3473735
X-RAY DIFFRACTIONf_chiral_restr0.056374
X-RAY DIFFRACTIONf_plane_restr0.007475
X-RAY DIFFRACTIONf_dihedral_angle_d13.828989
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.57-1.60930.351410.29723142328399
1.6093-1.65280.27211400.24923102324299
1.6528-1.70140.27741430.21623170331399
1.7014-1.75630.19031420.18353146328899
1.7563-1.81910.20961410.152531423283100
1.8191-1.89190.15861440.13033174331899
1.8919-1.9780.16391420.12873157329999
1.978-2.08230.16371420.12423152329499
2.0823-2.21270.14991440.11863192333699
2.2127-2.38340.16681430.12173180332399
2.3834-2.62310.16621430.12313160330399
2.6231-3.00230.1621450.13433208335399
3.0023-3.7810.15591440.13723203334797
3.781-27.57010.15891460.14933246339295

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