PDB-7stv: Crystal structure of sulfatase from Pedobacter yulinensis

ID or keywords:

Entry

Database: PDB / ID: 7stv

Title

Crystal structure of sulfatase from Pedobacter yulinensis

Components

N-acetylgalactosamine-6-sulfatase

Keywords

HYDROLASE

Function / homology

Function and homology information

arylsulfatase activity / metal ion binding
Similarity search - Function

Biological species

Pedobacter yulinensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

O'Malley, A. / Schlachter, C.R. / Grimes, L.L. / Tomashek, J.J. / Lee, A.L. / Chruszcz, M.

Funding support

1items

Citation

Journal: Molecules / Year: 2021
Title: Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis .
Authors: Schlachter, C.R. / O'Malley, A. / Grimes, L.L. / Tomashek, J.J. / Chruszcz, M. / Lee, L.A.

History

Deposition	Nov 15, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 26, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 2, 2022	Group: Database references / Category: citation / Item: _citation.title
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 15, 2023	Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7stv.cif.gz	179 KB	Display	PDBx/mmCIF format
PDB format	pdb7stv.ent.gz	135.4 KB	Display	PDB format
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Validation report

Summary document	7stv_validation.pdf.gz	852.2 KB	Display	wwPDB validaton report
Full document	7stv_full_validation.pdf.gz	857.8 KB	Display
Data in XML	7stv_validation.xml.gz	18.8 KB	Display
Data in CIF	7stv_validation.cif.gz	26.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/st/7stv ftp://data.pdbj.org/pub/pdb/validation_reports/st/7stv	HTTPS FTP

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Related structure data

Related structure data	7sttSC 7stuC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3l6q-d 2rch-d 1qs0-d 2nnb-d 6rzq-d 1jme-d 6eo4-d 7nqr-d 2rcm-d 3cli-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: N-acetylgalactosamine-6-sulfatase

hetero molecules

51.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-acetylgalactosamine-6-sulfatase

hetero molecules

A: N-acetylgalactosamine-6-sulfatase

hetero molecules

defined by author&software
Evidence: gel filtration
103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.728, 82.728, 115.292
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-505- CL
2	1	A-700- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	N-acetylgalactosamine-6-sulfatase Mass: 51392.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pedobacter yulinensis (bacteria) / Gene: C7T94_09545 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2T3HKC0

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Non-polymers , 5 types, 122 molecules

#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.5 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium citrate pH 5.5, 20% w/v polyethylene glycol 3000

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Data collection

Diffraction	Mean temperature: 295 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.34→40 Å / Num. obs: 19275 / % possible obs: 98.8 % / Redundancy: 9.2 % / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.101 / R_pim(I) all: 0.048 / R_rim(I) all: 0.148 / R_sym value: 0.101 / Net I/σ(I): 18.5
Reflection shell	Resolution: 2.34→2.38 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.489 / Mean I/σ(I) obs: 2 / Num. unique obs: 936 / CC_1/2: 0.948 / CC star: 0.986 / R_pim(I) all: 0.175 / R_rim(I) all: 0.525 / R_sym value: 0.489 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7STT

7stt

Resolution: 2.35→34.232 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.937 / SU B: 19.712 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.393 / ESU R Free: 0.244
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2295	943	4.904 %
R_work	0.1717	18285	-
all	0.174	-	-
obs	-	19228	98.353 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 56.402 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.062 Å²	1.031 Å²	0 Å²
2-	-	2.062 Å²	-0 Å²
3-	-	-	-6.691 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→34.232 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3448	0	18	116	3582

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	3550
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.015	3245
X-RAY DIFFRACTION	r_angle_refined_deg	1.313	1.651	4817
X-RAY DIFFRACTION	r_angle_other_deg	1.271	1.582	7471
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.423	5	437
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.863	22.256	195
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.266	15	561
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.733	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	444
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4093
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	857
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	767
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	3075
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	1721
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	1472
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	161
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.113	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.141	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.242	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.28	0.2	65
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.224	0.2	6
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.067	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.719	4.83	1754
X-RAY DIFFRACTION	r_mcbond_other	1.719	4.829	1753
X-RAY DIFFRACTION	r_mcangle_it	2.86	7.238	2189
X-RAY DIFFRACTION	r_mcangle_other	2.86	7.239	2190
X-RAY DIFFRACTION	r_scbond_it	1.864	5.014	1796
X-RAY DIFFRACTION	r_scbond_other	1.853	5.012	1793
X-RAY DIFFRACTION	r_scangle_it	3.163	7.422	2628
X-RAY DIFFRACTION	r_scangle_other	3.162	7.423	2629
X-RAY DIFFRACTION	r_lrange_it	5.182	56.394	4062
X-RAY DIFFRACTION	r_lrange_other	5.183	56.355	4055

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.35-2.411	0.301	77	0.286	1236	X-RAY DIFFRACTION	93.3191
2.411-2.477	0.352	58	0.274	1336	X-RAY DIFFRACTION	100
2.477-2.548	0.316	73	0.248	1253	X-RAY DIFFRACTION	99.9246
2.548-2.626	0.306	74	0.231	1235	X-RAY DIFFRACTION	98.7179
2.626-2.712	0.276	68	0.209	1190	X-RAY DIFFRACTION	99.9206
2.712-2.807	0.272	53	0.19	1175	X-RAY DIFFRACTION	100
2.807-2.912	0.279	51	0.184	1147	X-RAY DIFFRACTION	99.9166
2.912-3.03	0.187	67	0.174	1068	X-RAY DIFFRACTION	100
3.03-3.164	0.23	50	0.18	1055	X-RAY DIFFRACTION	99.8193
3.164-3.318	0.325	49	0.187	1002	X-RAY DIFFRACTION	99.3384
3.318-3.496	0.221	29	0.184	953	X-RAY DIFFRACTION	98.4955
3.496-3.706	0.208	49	0.158	878	X-RAY DIFFRACTION	97.1698
3.706-3.96	0.239	47	0.156	834	X-RAY DIFFRACTION	96.4951
3.96-4.273	0.145	44	0.132	751	X-RAY DIFFRACTION	94.5303
4.273-4.676	0.182	37	0.128	702	X-RAY DIFFRACTION	95.232
4.676-5.219	0.252	32	0.138	672	X-RAY DIFFRACTION	98.0501
5.219-6.009	0.197	32	0.163	599	X-RAY DIFFRACTION	98.9028
6.009-7.319	0.233	27	0.16	509	X-RAY DIFFRACTION	98.893
7.319-10.181	0.191	22	0.136	422	X-RAY DIFFRACTION	99.1071
10.181-34.232	0.291	4	0.192	268	X-RAY DIFFRACTION	98.1949

Refinement TLS params.

Method: refined / Origin x: -33.34 Å / Origin y: 6.47 Å / Origin z: -16.9122 Å

	11	12	13	21	22	23	31	32	33
T	0.0866 Å²	0.0344 Å²	-0.0179 Å²	-	0.0973 Å²	-0.0188 Å²	-	-	0.0134 Å²
L	0.7211 °²	-0.1627 °²	-0.1402 °²	-	0.9915 °²	-0.3944 °²	-	-	0.7423 °²
S	-0.135 Å °	-0.1441 Å °	0.016 Å °	0.1245 Å °	0.0798 Å °	-0.1028 Å °	-0.0659 Å °	0.0496 Å °	0.0553 Å °

Refinement TLS group

Selection: ALL

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