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- PDB-8vg9: Crystallographic structure of Ruminococcus champanellensis xylana... -

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Basic information

Entry
Database: PDB / ID: 8vg9
TitleCrystallographic structure of Ruminococcus champanellensis xylanase (RcXyn30A)
ComponentsO-Glycosyl hydrolase
KeywordsHYDROLASE / Xylanase / GH30 / Ruminococcus champanellensis
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily ...: / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Esterase-like / Putative esterase / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold / Glycoside hydrolase superfamily
Similarity search - Domain/homology
FLUORIDE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / O-Glycosyl hydrolase
Similarity search - Component
Biological speciesRuminococcus champanellensis 18P13 = JCM 17042 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsVacilotto, M.M. / Araujo, E.A. / Polikarpov, I.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/08780-1 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)306852/2021-7 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)440180/2022-8 Brazil
CitationJournal: To Be Published
Title: Crystallographic structure of Ruminococcus champanellensis xylanase (RcXyn30A)
Authors: Vacilotto, M.M. / Araujo, E.A. / Polikarpov, I.
History
DepositionDec 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-Glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,06814
Polymers46,5831
Non-polymers48513
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.620, 55.019, 63.329
Angle α, β, γ (deg.)90.000, 95.160, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein O-Glycosyl hydrolase / Xylanase


Mass: 46583.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus champanellensis 18P13 = JCM 17042 (bacteria)
Strain: 18P13 = JCM 17042 / Gene: RUM_18530 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: D4LE58

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Non-polymers , 6 types, 487 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 37.5% (v/v) precipitants agents (25% (v/v) MPD, 25% (w/v) PEG 1000 and 25% (w/v) PEG 3350), 0.1 M buffer solution (TRIS base/bicine) pH 8.5 and 0.09 M halogens

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.37→44.05 Å / Num. obs: 81497 / % possible obs: 99.87 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.42 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1003 / Rpim(I) all: 0.04215 / Rrim(I) all: 0.109 / Net I/σ(I): 11.53
Reflection shellResolution: 1.37→1.419 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.8854 / Num. unique obs: 8035 / CC1/2: 0.667 / CC star: 0.894 / Rpim(I) all: 0.3613 / Rrim(I) all: 0.8861 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→44.05 Å / SU ML: 0.1231 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.1095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.164 4076 5 %
Rwork0.14 77421 -
obs0.1412 81497 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.24 Å2
Refinement stepCycle: LAST / Resolution: 1.37→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 26 474 3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623312
X-RAY DIFFRACTIONf_angle_d0.91034522
X-RAY DIFFRACTIONf_chiral_restr0.0844469
X-RAY DIFFRACTIONf_plane_restr0.0101602
X-RAY DIFFRACTIONf_dihedral_angle_d6.9752460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.31931340.26352534X-RAY DIFFRACTION94.11
1.39-1.40.27531370.21242605X-RAY DIFFRACTION99.56
1.4-1.420.21131410.18592677X-RAY DIFFRACTION99.72
1.42-1.440.20771410.17642681X-RAY DIFFRACTION100
1.44-1.460.20551390.17472634X-RAY DIFFRACTION100
1.46-1.480.2081400.16772661X-RAY DIFFRACTION100
1.48-1.50.21341400.15592666X-RAY DIFFRACTION100
1.5-1.520.20071410.15782675X-RAY DIFFRACTION99.96
1.52-1.550.17651400.14872658X-RAY DIFFRACTION100
1.55-1.580.17111410.13822678X-RAY DIFFRACTION100
1.58-1.60.16531380.13052636X-RAY DIFFRACTION100
1.6-1.640.17251410.12232667X-RAY DIFFRACTION100
1.64-1.670.13631410.11832691X-RAY DIFFRACTION100
1.67-1.710.15811410.11792673X-RAY DIFFRACTION100
1.71-1.750.15611400.1182657X-RAY DIFFRACTION100
1.75-1.790.16131410.12412676X-RAY DIFFRACTION100
1.79-1.840.16821410.12692678X-RAY DIFFRACTION100
1.84-1.890.17611410.13032676X-RAY DIFFRACTION100
1.89-1.950.15361400.12132657X-RAY DIFFRACTION99.96
1.95-2.020.16441410.12752679X-RAY DIFFRACTION99.89
2.02-2.10.15031400.12972672X-RAY DIFFRACTION99.93
2.1-2.20.15151410.132679X-RAY DIFFRACTION99.86
2.2-2.310.19241410.13632666X-RAY DIFFRACTION99.93
2.31-2.460.15311410.14322688X-RAY DIFFRACTION99.89
2.46-2.650.17461410.14722680X-RAY DIFFRACTION99.93
2.65-2.920.15471420.14732697X-RAY DIFFRACTION100
2.92-3.340.17031420.152698X-RAY DIFFRACTION99.96
3.34-4.20.13021430.12782710X-RAY DIFFRACTION99.83
4.2-44.050.13571460.13952772X-RAY DIFFRACTION99.86

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