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- PDB-6j66: Chondroitin sulfate/dermatan sulfate endolytic 4-O-sulfatase -

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Basic information

Entry
Database: PDB / ID: 6j66
TitleChondroitin sulfate/dermatan sulfate endolytic 4-O-sulfatase
ComponentsChondroitin sulfate/dermatan sulfate 4-O-endosulfatase protein
KeywordsHYDROLASE / glycosaminoglycan / chondroitin sulfate / dermatan sulfate / sulfatase
Function / homology
Function and homology information


sulfuric ester hydrolase activity
Similarity search - Function
Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chondroitin sulfate/dermatan sulfate 4-O-endosulfatase protein
Similarity search - Component
Biological speciesVibrio sp. FC509 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å
AuthorsGu, L. / Li, F. / Su, T. / Wang, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNos. 31570071 China
National Natural Science Foundation of ChinaNos. 31800665 China
CitationJournal: Front Microbiol / Year: 2019
Title: Comparative Study of Two Chondroitin Sulfate/Dermatan Sulfate 4-O-Sulfatases With High Identity.
Authors: Wang, S. / Su, T. / Zhang, Q. / Guan, J. / He, J. / Gu, L. / Li, F.
History
DepositionJan 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chondroitin sulfate/dermatan sulfate 4-O-endosulfatase protein
B: Chondroitin sulfate/dermatan sulfate 4-O-endosulfatase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2924
Polymers119,2122
Non-polymers802
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size-exclusion chromatography analysis revealed the endo-4-O-sulfatase primarily existed as a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-13 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.426, 107.732, 87.569
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chondroitin sulfate/dermatan sulfate 4-O-endosulfatase protein


Mass: 59606.059 Da / Num. of mol.: 2 / Mutation: C96FGly
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio sp. FC509 (bacteria) / Plasmid: pET-30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0C5AQI9, N-acetylgalactosamine-4-sulfatase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPS (pH 7.5), 20% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 75093 / % possible obs: 99.2 % / Redundancy: 3.6 % / Net I/σ(I): 26.21
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QZU

2qzu


Resolution: 1.953→37.915 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.57
RfactorNum. reflection% reflection
Rfree0.2142 3765 5.02 %
Rwork0.1805 --
obs0.1823 74927 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.953→37.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7755 0 2 511 8268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077995
X-RAY DIFFRACTIONf_angle_d0.90310870
X-RAY DIFFRACTIONf_dihedral_angle_d14.0794742
X-RAY DIFFRACTIONf_chiral_restr0.0541100
X-RAY DIFFRACTIONf_plane_restr0.0061435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9534-1.97810.33281220.26582465X-RAY DIFFRACTION93
1.9781-2.00410.2721340.24112643X-RAY DIFFRACTION99
2.0041-2.03160.2751510.22912665X-RAY DIFFRACTION100
2.0316-2.06060.26871380.25022603X-RAY DIFFRACTION99
2.0606-2.09140.33161210.28782621X-RAY DIFFRACTION97
2.0914-2.1240.28271450.22532579X-RAY DIFFRACTION99
2.124-2.15880.27761450.21322676X-RAY DIFFRACTION99
2.1588-2.19610.26421380.20142636X-RAY DIFFRACTION99
2.1961-2.2360.30811390.24112652X-RAY DIFFRACTION99
2.236-2.2790.39221290.30422589X-RAY DIFFRACTION97
2.279-2.32550.27031300.20392657X-RAY DIFFRACTION99
2.3255-2.37610.20011190.19212651X-RAY DIFFRACTION99
2.3761-2.43130.21591380.18842636X-RAY DIFFRACTION99
2.4313-2.49210.21621420.18862647X-RAY DIFFRACTION99
2.4921-2.55950.22871480.19332643X-RAY DIFFRACTION99
2.5595-2.63480.24411530.19492599X-RAY DIFFRACTION99
2.6348-2.71980.24931440.18822646X-RAY DIFFRACTION99
2.7198-2.8170.21341530.18182670X-RAY DIFFRACTION100
2.817-2.92970.24051390.18752641X-RAY DIFFRACTION99
2.9297-3.0630.20621470.18952658X-RAY DIFFRACTION99
3.063-3.22440.20911390.18422627X-RAY DIFFRACTION99
3.2244-3.42630.24151250.18282667X-RAY DIFFRACTION99
3.4263-3.69070.1781560.17162636X-RAY DIFFRACTION99
3.6907-4.06170.17711430.15012638X-RAY DIFFRACTION98
4.0617-4.64850.15451390.12252660X-RAY DIFFRACTION98
4.6485-5.85320.15091410.13852671X-RAY DIFFRACTION100
5.8532-37.92190.1751470.14542686X-RAY DIFFRACTION98

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