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- PDB-6q2f: Structure of Rhamnosidase from Novosphingobium sp. PP1Y -

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Basic information

Entry
Database: PDB / ID: 6q2f
TitleStructure of Rhamnosidase from Novosphingobium sp. PP1Y
ComponentsGlycoside hydrolase family protein
KeywordsHYDROLASE / rhamnosidase / RHA-P / glycosyl hydrolase
Function / homologyalpha-L-rhamnosidase / Galactose-binding-like domain superfamily / hydrolase activity / Glycoside hydrolase family protein
Function and homology information
Biological speciesNovosphingobium sp. PP1Y (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.20000074944 Å
AuthorsTerry, B. / Ha, J. / Izzo, V. / Sazinsky, M.H.
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: The crystal structure and insight into the substrate specificity of the alpha-L rhamnosidase RHA-P from Novosphingobium sp. PP1Y.
Authors: Terry, B. / Ha, J. / De Lise, F. / Mensitieri, F. / Izzo, V. / Sazinsky, M.H.
History
DepositionAug 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0362
Polymers126,0131
Non-polymers231
Water13,187732
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)80.809, 114.570, 158.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Glycoside hydrolase family protein


Mass: 126012.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium sp. PP1Y (bacteria) / Gene: PP1Y_Mpl10172 / Production host: Escherichia coli (E. coli) / References: UniProt: F6IEX3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.8, 6-7% Tascimate pH 5.0, 2-10 mM Tris, pH 7.5, 10 % w/w PEG 20K, 6-10% glycerol, and 0.01% NaN3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.20000074944→39.7 Å / Num. obs: 144262 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.4712029358 Å2 / Rsym value: 0.092 / Net I/σ(I): 14.2
Reflection shellResolution: 2.20000074944→2.25 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 29836 / Rsym value: 0.462

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.20000074944→39.69925 Å / SU ML: 0.18921853219 / Cross valid method: FREE R-VALUE / σ(F): 1.89205264243 / Phase error: 18.4318606734
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.177046121509 6975 4.83495307149 %
Rwork0.162851787376 137287 -
obs0.163541015328 144262 99.7986897539 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.4570003117 Å2
Refinement stepCycle: LAST / Resolution: 2.20000074944→39.69925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8079 0 1 732 8812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009943882976888282
X-RAY DIFFRACTIONf_angle_d1.0265087913811294
X-RAY DIFFRACTIONf_chiral_restr0.06871530251821242
X-RAY DIFFRACTIONf_plane_restr0.005997329077061483
X-RAY DIFFRACTIONf_dihedral_angle_d16.32457782652972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.20000074944-2.2250.2648762156642420.2288226797714536X-RAY DIFFRACTION99.1080688654
2.225-2.25120.2189933706952260.2170191597864588X-RAY DIFFRACTION99.813394153
2.2512-2.27860.2364475998552230.211991923674520X-RAY DIFFRACTION99.9157362545
2.2786-2.30750.2610265516652290.2133196354664670X-RAY DIFFRACTION99.8369675973
2.3075-2.33780.2213821686532170.2049863991614566X-RAY DIFFRACTION99.6873697374
2.3378-2.36980.2243148066522440.2027369767064527X-RAY DIFFRACTION99.8743981578
2.3698-2.40370.2083341436112000.1932444761944597X-RAY DIFFRACTION99.6468633153
2.4037-2.43960.2312542858892540.1975111288154609X-RAY DIFFRACTION99.815270936
2.4396-2.47770.2279784417612570.1920322057334499X-RAY DIFFRACTION99.7692469058
2.4777-2.51830.2082561172092640.1874619854854542X-RAY DIFFRACTION99.4413407821
2.5183-2.56170.2210083841952250.1772440029594576X-RAY DIFFRACTION99.93755204
2.5617-2.60830.2034063912992440.1728940557324620X-RAY DIFFRACTION99.9178307313
2.6083-2.65840.2175053294042470.1728629867944513X-RAY DIFFRACTION99.7903563941
2.6584-2.71270.1650301795442290.1654183127564609X-RAY DIFFRACTION99.9173895085
2.7127-2.77170.1870025094432200.1696774601564563X-RAY DIFFRACTION99.895572264
2.7717-2.83610.1796054132622250.1697855312174593X-RAY DIFFRACTION99.9170468685
2.8361-2.9070.2138766577742660.1734297244684566X-RAY DIFFRACTION99.7111019397
2.907-2.98560.1806271938642030.1692382796424627X-RAY DIFFRACTION99.8552821997
2.9856-3.07340.2073012579562070.163805248024571X-RAY DIFFRACTION99.5624088352
3.0734-3.17260.151162327592420.1654880159054555X-RAY DIFFRACTION99.9166840242
3.1726-3.28590.1746053661172400.1650392488434573X-RAY DIFFRACTION99.896222499
3.2859-3.41740.1568616359932160.1654910008594626X-RAY DIFFRACTION100
3.4174-3.57290.1636936458872130.1622002344814584X-RAY DIFFRACTION99.9375
3.5729-3.76110.1579655777162620.1586027222294535X-RAY DIFFRACTION99.895876718
3.7611-3.99650.1609073822922350.1414628966794611X-RAY DIFFRACTION99.7940691928
3.9965-4.30480.1579777312812390.1281036756374568X-RAY DIFFRACTION99.9584113121
4.3048-4.73730.1261297799582660.11995790064553X-RAY DIFFRACTION99.9377851514
4.7373-5.42140.1317748463022150.1350523123484610X-RAY DIFFRACTION99.9585663973
5.4214-6.82470.1638506344752220.1660559293554583X-RAY DIFFRACTION99.896049896
6.8247-39.699250.1906883431852030.1644597556464597X-RAY DIFFRACTION99.3994615862
Refinement TLS params.Method: refined / Origin x: 17.8974766958 Å / Origin y: 84.3774061966 Å / Origin z: 40.635997745 Å
111213212223313233
T0.16789562596 Å2-0.0373769558086 Å20.0432800514563 Å2-0.23909939371 Å20.0190179729423 Å2--0.247619772596 Å2
L0.367933493793 °2-0.101185137944 °20.120449879495 °2-0.783316649126 °2-0.0384502686008 °2--0.948479878961 °2
S0.0249456678424 Å °0.0280912430705 Å °0.0416993100021 Å °-0.0920339620328 Å °-0.0374674081492 Å °-0.155073865972 Å °-0.0564770351081 Å °0.24263730953 Å °0.00184813531781 Å °
Refinement TLS groupSelection details: all

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