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- PDB-6prm: Crystal structure of apo PsS1_19B -

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Basic information

Entry
Database: PDB / ID: 6prm
TitleCrystal structure of apo PsS1_19B
Componentsexo-4S-kappa carrageenan S1 sulfatase
KeywordsHYDROLASE / S1 sulfatase
Function / homologysulfuric ester hydrolase activity / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Sulfatase
Function and homology information
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHettle, A.G. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Commun Biol / Year: 2019
Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.
Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 11, 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: exo-4S-kappa carrageenan S1 sulfatase
B: exo-4S-kappa carrageenan S1 sulfatase
C: exo-4S-kappa carrageenan S1 sulfatase
D: exo-4S-kappa carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,4318
Polymers212,2714
Non-polymers1604
Water1,874104
1
A: exo-4S-kappa carrageenan S1 sulfatase
B: exo-4S-kappa carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2154
Polymers106,1352
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-10 kcal/mol
Surface area29900 Å2
MethodPISA
2
C: exo-4S-kappa carrageenan S1 sulfatase
D: exo-4S-kappa carrageenan S1 sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2154
Polymers106,1352
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-3 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.510, 88.580, 106.600
Angle α, β, γ (deg.)82.220, 79.850, 84.200
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROAA27 - 47323 - 469
21SERSERPROPROBB27 - 47323 - 469
12SERSERPROPROAA27 - 47323 - 469
22SERSERPROPROCC27 - 47323 - 469
13LYSLYSGLNGLNAA28 - 47224 - 468
23LYSLYSGLNGLNDD28 - 47224 - 468
14SERSERPROPROBB27 - 47323 - 469
24SERSERPROPROCC27 - 47323 - 469
15LYSLYSGLNGLNBB28 - 47224 - 468
25LYSLYSGLNGLNDD28 - 47224 - 468
16LYSLYSGLNGLNCC28 - 47224 - 468
26LYSLYSGLNGLNDD28 - 47224 - 468

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
exo-4S-kappa carrageenan S1 sulfatase


Mass: 53067.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Strain: PS47 / Gene: EU509_08890 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A063KLJ9*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→104.2 Å / Num. obs: 58432 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.57 Å / Rmerge(I) obs: 0.334 / Num. unique obs: 4508

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BIA

6bia


Resolution: 2.5→47.6 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.866 / SU B: 13.753 / SU ML: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.353
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 2912 5 %RANDOM
Rwork0.2376 ---
obs0.2393 55519 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.88 Å2 / Biso mean: 30.899 Å2 / Biso min: 4.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å2-1.26 Å21.48 Å2
2--0.9 Å21.41 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 2.5→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13985 0 4 104 14093
Biso mean--37.19 19.3 -
Num. residues----1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01314360
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712828
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.65119437
X-RAY DIFFRACTIONr_angle_other_deg1.1931.58229780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56251789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50622.462780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.094152327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7291588
X-RAY DIFFRACTIONr_chiral_restr0.0560.21754
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216394
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023166
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A151330.02
12B151330.02
21A151830.02
22C151830.02
31A151520.03
32D151520.03
41B151290.02
42C151290.02
51B151440.02
52D151440.02
61C151440.03
62D151440.03
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 192 -
Rwork0.308 4094 -
all-4286 -
obs--96.34 %

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