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- PDB-8oug: Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus -

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Basic information

Entry
Database: PDB / ID: 8oug
TitleExo-beta-d-glucosaminidase from Pyrococcus chitonophagus
ComponentsBeta-galactosidase
KeywordsHYDROLASE / hyperthermophile
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesThermococcus chitonophagus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRypniewski, W. / Biniek-Antosiak, K. / Bejger, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUM-2017/27/B/NZ1/02201 Poland
CitationJournal: To Be Published
Title: Exo-beta-d-glucosaminidase from Pyrococcus chitonophagus
Authors: Rypniewski, W. / Biniek-Antosiak, K. / Bejger, M.
History
DepositionApr 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 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: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,91730
Polymers91,1441
Non-polymers1,77329
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint73 kcal/mol
Surface area27550 Å2
Unit cell
Length a, b, c (Å)89.400, 120.500, 145.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-925-

HOH

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Components

#1: Protein Beta-galactosidase /


Mass: 91143.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus chitonophagus (archaea) / Gene: A3L04_10820 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A160VTD9
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 308 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG buffer pH 8.0, 25% v/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 46003 / % possible obs: 99.5 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 19.43
Reflection shellResolution: 2.1→2.23 Å / Num. unique obs: 7306 / CC1/2: 0.839

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.42 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.955 / SU B: 15.881 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 998 2.2 %RANDOM
Rwork0.165 ---
obs0.1662 44987 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.13 Å2 / Biso mean: 47.76 Å2 / Biso min: 32.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å2-0 Å2
2--2.2 Å20 Å2
3----1.68 Å2
Refinement stepCycle: final / Resolution: 2.1→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6445 0 117 208 6770
Biso mean--68.84 53.59 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136721
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176234
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6539075
X-RAY DIFFRACTIONr_angle_other_deg1.3351.57214429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1615779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43122.366372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.441151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9511539
X-RAY DIFFRACTIONr_chiral_restr0.0830.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021472
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 72 -
Rwork0.323 3264 -
all-3336 -
obs--98.7 %
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)
10.62080.1716-0.11231.2094-0.03261.03420.0123-0.01010.08380.062-0.0117-0.0031-0.2451-0.0215-0.00060.4516-0.0027-0.00210.1901-0.02790.015826.914415.540417.8071
21.34620.40370.17471.40980.17622.97220.0688-0.1201-0.24210.1564-0.0085-0.09240.39940.0816-0.06030.44690.0135-0.0060.17690.01990.052932.4858-18.3620.5834
34.3997-0.2204-1.14841.96330.35312.46590.0420.0978-0.17690.1108-0.15670.3810.0428-0.59020.11470.3675-0.03840.04180.4764-0.05630.0901-4.4694-4.174620.5742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 494
2X-RAY DIFFRACTION2A495 - 650
3X-RAY DIFFRACTION3A651 - 780

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