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- PDB-8gyg: Purification ,Crystallization and X-ray Diffraction analysis of a... -

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Basic information

Entry
Database: PDB / ID: 8gyg
TitlePurification ,Crystallization and X-ray Diffraction analysis of a novel arysulfatase from Pseudoalteromonas atlantica T6c
ComponentsArysulfatase
KeywordsHYDROLASE / Arysulfatase / Crystal
Function / homology:
Function and homology information
Biological speciesPseudoalteromonas atlantica T6c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, P.P. / Wu, Y.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Purification ,Crystallization and X-ray Diffraction analysis of a novel arysulfatase from Pseudoalteromonas atlantica T6c
Authors: Dong, P.P. / Wu, Y.K.
History
DepositionSep 22, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arysulfatase
B: Arysulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9007
Polymers66,6852
Non-polymers2155
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-94 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.170, 61.380, 89.600
Angle α, β, γ (deg.)90.000, 97.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arysulfatase


Mass: 33342.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas atlantica T6c (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.27 Å3/Da / Density % sol: 45.89 % / Description: strip
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2o%PEG 3350, 0.2M Sodium Thiocyamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.55→38.61 Å / Num. obs: 85833 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.3
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 1.077 / Num. unique obs: 6332 / CC1/2: 0.528

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6nks

6nks


Resolution: 2→29.585 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 1965 4.9 %
Rwork0.2004 38105 -
obs0.2025 40070 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.52 Å2 / Biso mean: 23.9035 Å2 / Biso min: 7.36 Å2
Refinement stepCycle: final / Resolution: 2→29.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 5 612 5202
Biso mean--19.41 29.24 -
Num. residues----596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.29941380.2552709100
2.05-2.10540.3061460.2488267999
2.1054-2.16740.30771460.252678100
2.1674-2.23730.27161430.24642731100
2.2373-2.31720.30781340.24692713100
2.3172-2.410.31091200.2407272199
2.41-2.51960.31341450.2423269999
2.5196-2.65230.28781480.2246270299
2.6523-2.81840.23581340.2149269999
2.8184-3.03580.27661490.2134270599
3.0358-3.34090.2441430.20162723100
3.3409-3.82350.18571510.16742743100
3.8235-4.81390.1861250.14232767100
4.8139-290.18761430.16492836100

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