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- PDB-7drq: Crystal structure of polysaccharide lyase Uly1 -

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Basic information

Entry
Database: PDB / ID: 7drq
TitleCrystal structure of polysaccharide lyase Uly1
ComponentsUly1
KeywordsLYASE / ulvan lyase / polysaccharide lyase family 24 / marine bacterium
Function / homologyBNR repeat-containing family member / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesCatenovulum maritimum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsChen, X.L. / Cao, H.Y. / Xu, F. / Dong, F.
CitationJournal: Appl.Environ.Microbiol. / Year: 2021
Title: Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24.
Authors: Xu, F. / Dong, F. / Sun, X.H. / Cao, H.Y. / Fu, H.H. / Li, C.Y. / Zhang, X.Y. / McMinn, A. / Zhang, Y.Z. / Wang, P. / Chen, X.L.
History
DepositionDec 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uly1
B: Uly1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0107
Polymers114,8102
Non-polymers2005
Water25,2031399
1
A: Uly1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5254
Polymers57,4051
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-36 kcal/mol
Surface area19660 Å2
MethodPISA
2
B: Uly1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4853
Polymers57,4051
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-36 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.993, 99.998, 95.304
Angle α, β, γ (deg.)90.000, 90.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uly1


Mass: 57404.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenovulum maritimum (bacteria) / Gene: XM47_11230 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J8GWN9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1399 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM calcium acetate, 100 mM MES (pH 6.0), 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.79→37.11 Å / Num. obs: 101227 / % possible obs: 99.16 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.049 / Rrim(I) all: 0.128 / Net I/σ(I): 22.79
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 7 % / Rmerge(I) obs: 0.286 / Num. unique obs: 9595 / Rpim(I) all: 0.116 / Rrim(I) all: 0.309 / % possible all: 94.48

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→37.11 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1824 4900 4.84 %
Rwork0.1572 96294 -
obs0.1585 101194 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.05 Å2 / Biso mean: 19.1079 Å2 / Biso min: 4.89 Å2
Refinement stepCycle: final / Resolution: 1.79→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7701 0 5 1399 9105
Biso mean--26.89 28.96 -
Num. residues----960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.79-1.810.23961400.19782781292185
1.81-1.830.2341680.19253153332199
1.83-1.860.21181760.18233177335399
1.86-1.880.20761770.17283187336499
1.88-1.90.22131830.16873191337499
1.9-1.930.19751320.16243259339199
1.93-1.960.19661350.16043181331699
1.96-1.990.20961470.16223254340199
1.99-2.020.18621680.15883195336399
2.02-2.050.19521750.15823202337799
2.05-2.090.17041890.158932003389100
2.09-2.120.20751700.16131913361100
2.12-2.160.21222020.158431983400100
2.16-2.210.20871450.157632153360100
2.21-2.260.1951410.159132573398100
2.26-2.310.19031740.154532223396100
2.31-2.370.21921250.159732393364100
2.37-2.430.21861630.162732443407100
2.43-2.50.19931540.164132353389100
2.5-2.580.20171480.160832243372100
2.58-2.680.21141560.16332443400100
2.68-2.780.19681710.164732383409100
2.78-2.910.16561600.165432593419100
2.91-3.060.19181600.159732503410100
3.06-3.250.17621620.154232203382100
3.25-3.510.15391480.147232463394100
3.51-3.860.1471590.143532953454100
3.86-4.410.15061870.132132233410100
4.42-5.560.14622220.134832153437100
5.56-37.110.18661630.18643299346299

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