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- PDB-6bia: Crystal structure of Ps i-CgsB -

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Basic information

Entry
Database: PDB / ID: 6bia
TitleCrystal structure of Ps i-CgsB
ComponentsSulfatase
KeywordsOXIDOREDUCTASE / S1 sulfatase
Function / homologysulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / CITRIC ACID / Sulfatase
Function and homology information
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsHettle, A.G. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: Structure / Year: 2018
Title: The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme.
Authors: Hettle, A.G. / Vickers, C. / Robb, C.S. / Liu, F. / Withers, S.G. / Hehemann, J.H. / Boraston, A.B.
#1: Journal: To Be Published
Title: The molecular basis of polysaccharide sulfatase activity and a nomenclature for catalytic subsides in this class of enzyme.
Authors: Hettle, A.G. / Boraston, A.B.
History
DepositionNov 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfatase
B: Sulfatase
C: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,10412
Polymers162,2223
Non-polymers8839
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-9 kcal/mol
Surface area48500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.850, 133.850, 223.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLYSLYSAA28 - 47725 - 474
21GLNGLNLYSLYSBB28 - 47725 - 474
12LYSLYSLYSLYSAA29 - 47726 - 474
22LYSLYSLYSLYSCC29 - 47726 - 474
13LYSLYSTHRTHRBB29 - 47826 - 475
23LYSLYSTHRTHRCC29 - 47826 - 475

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Sulfatase /


Mass: 54073.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Gene: DC53_12720 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A063KPH1
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.65 / Details: PEG 3350, citric acid, arginine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.8→114.86 Å / Num. obs: 50781 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.074 / Net I/σ(I): 13.7
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4582 / CC1/2: 0.912 / Rpim(I) all: 0.356 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B0K

6b0k


Resolution: 2.8→114.86 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.949 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.161 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 2464 5 %RANDOM
Rwork0.2384 ---
obs0.2397 46901 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.5 Å2 / Biso mean: 45.879 Å2 / Biso min: 1.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.8→114.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10671 0 54 61 10786
Biso mean--63.79 25.88 -
Num. residues----1354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911034
X-RAY DIFFRACTIONr_bond_other_d0.0010.029565
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.92914974
X-RAY DIFFRACTIONr_angle_other_deg0.939322255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0751351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32324.565552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.223151697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.641545
X-RAY DIFFRACTIONr_chiral_restr0.0750.21527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022314
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A304020.04
12B304020.04
21A302440.05
22C302440.05
31B302400.04
32C302400.04
LS refinement shellResolution: 2.799→2.871 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 160 -
Rwork0.407 3382 -
all-3542 -
obs--96.02 %

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