PDB-2cfu: Crystal structure of SdsA1, an alkylsulfatase from Pseudomonas ae...

ID or keywords:

Entry

Database: PDB / ID: 2cfu

Title

Crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, in complex with 1-decane-sulfonic-acid.

Components

SDSA1

Keywords

HYDROLASE / SDS-HYDROLASE / SDSA1 /

LACTAMASE

Function / homology

Function and homology information

linear primary-alkylsulfatase / linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / outer membrane-bounded periplasmic space /

protein dimerization activity / identical protein binding /

metal ion binding
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Hagelueken, G. / Adams, T.M. / Wiehlmann, L. / Widow, U. / Kolmar, H. / Tuemmler, B. / Heinz, D.W. / Schubert, W.-D.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: The Crystal Structure of Sdsa1, an Alkylsulfatase from Pseudomonas Aeruginosa, Defines a Third Class of Sulfatases.
Authors: Hagelueken, G. / Adams, T.M. / Wiehlmann, L. / Widow, U. / Kolmar, H. / Tummler, B. / Heinz, D.W. / Schubert, W.-D.

History

Deposition	Feb 23, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 26, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 28, 2011	Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2cfu.cif.gz	156.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2cfu.ent.gz	123.8 KB	Display	PDB format
PDBx/mmJSON format	2cfu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/2cfu ftp://data.pdbj.org/pub/pdb/validation_reports/cf/2cfu	HTTPS FTP

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Related structure data

Related structure data	2cfzC 2cg2C 2cg3SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2cg3-1 2cg2-1 5a23-2 2cfz-1 5aij-1 5a23-1 5ajl-d 320 4axh-d 5wzq-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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #105 - Sep 2008 Ribonuclease A similarity (2) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: SDSA1

hetero molecules

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

1

A: SDSA1

hetero molecules

A: SDSA1

hetero molecules

defined by author&software
148 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.057, 86.057, 364.413
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

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Protein , 1 types, 1 molecules A

#1: Protein	SDSA1 / PROBABLE BETA-LACTAMASE Mass: 72673.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9I5I9

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Non-polymers , 5 types, 549 molecules

#2: Chemical	ChemComp-1DB / 1-DECANE-SULFONIC-ACID / DECANE-1-SULFONIC ACID Mass: 222.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₃S
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.7 %
Crystal grow	pH: 6 Details: 12% PEG 4000,10 % ISO-PROPANOL, 200 MM LICL,100 MM CITRATE PH6, pH 6.00

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9001
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 20, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9001 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 68233 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / R_merge(I) obs: 0.12 / Net I/σ(I): 12
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 7 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 3.1 / % possible all: 98

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CG3

2cg3

Resolution: 1.9→74.54 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.935 / SU B: 5.701 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. RESIDUES 206-208 ARE DISORDERED AND WERE MODELLED BY WATER. CHAIN B 1-6.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.217	3232	5.1 %	RANDOM
R_work	0.171	-	-	-
obs	0.174	60052	98.4 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 19.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.65 Å²	-0.32 Å²	0 Å²
2-	-	-0.65 Å²	0 Å²
3-	-	-	0.97 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→74.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4906	0	76	537	5519

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	5403
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.482	1.976	7349
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.109	5	693
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.801	22.918	281
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.307	15	884
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.82	15	65
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	773
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4290
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	2627
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	3643
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	549
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.051	0.2	4
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.171	0.2	153
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.148	0.2	50
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.436	2	3390
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.083	3	5259
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.902	2	2310
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.955	3	2075
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.261	232	-
R_work	0.205	4305	-
obs	-	-	97.8 %

Refinement TLS params.

Method: refined / Origin x: 37.953 Å / Origin y: 23.049 Å / Origin z: 173.386 Å / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)
1	1.4389	0.633	0.1151	0.836	-0.3762	0.336	-0.0559	0.0288	0.1715	0.0475	-0.0008	0.0521	0.0699	0.0091	0.0567	-0.1371	0.0193	-0.0022	-0.1397	0.001	-0.1471
2	1.3519	0.8809	-0.0944	1.5434	0.4523	0.5096	-0.0403	0.1198	-0.0977	-0.0408	0.1458	-0.1243	0.0055	0.0083	-0.1055	-0.144	-0.0046	0.0114	-0.124	-0.0165	-0.1476
3	0.7123	0.4492	0.2602	1.7185	0.2308	0.5185	0.0154	-0.0183	0.042	-0.0821	0.0246	0.1431	-0.0344	0.0227	-0.04	-0.1527	-0.0036	-0.0087	-0.1334	0.0091	-0.1427
4	1.0322	0.468	-0.285	1.8416	0.2912	0.9759	-0.0571	0.0463	-0.067	0.0612	-0.016	0.1067	0.0706	-0.0497	0.0731	-0.1375	0.0148	-0.0004	-0.1393	-0.0078	-0.1431
5	0.6966	-0.3632	0.5501	0.2415	-0.0211	1.7893	0.0684	-0.1435	-0.0749	-0.0138	0.0529	0.0901	0.246	-0.1287	-0.1213	-0.141	0.0079	0.0045	-0.1432	-0.0006	-0.1439
6	0.5454	0.0346	0.1954	0.0498	0.1446	0.437	0.0233	-0.0295	-0.0457	0.023	0.0049	0.0293	0.0294	-0.0002	-0.0282	-0.1081	0.0039	0.0107	-0.1295	-0.014	-0.1223
7	0.3136	0.1048	0.018	0.9673	0.326	0.4172	-0.0006	-0.0537	0.0129	0.0596	-0.0876	0.1223	-0.0002	0.0097	0.0882	-0.1394	0.0078	0.0092	-0.1475	-0.0192	-0.1171
8	0.3339	0.0324	0.1053	0.2163	-0.0794	0.7453	0.0063	-0.0774	0.0169	0.0538	-0.0361	-0.0291	-0.1147	0.042	0.0298	-0.127	-0.0036	-0.0021	-0.1464	-0.0075	-0.1475
9	0.7063	0.1221	0.2891	0.5693	0.025	1.1377	-0.0359	-0.016	0.0481	0.0871	-0.0092	-0.0983	-0.1289	0.1718	0.045	-0.1246	-0.0092	-0.0015	-0.1474	-0.0057	-0.1508
10	2.9554	0.7827	-2.4224	0.6792	-0.0867	2.6379	0.1827	-0.6098	0.6416	-0.3551	-0.2802	0.8163	0.0055	0.0757	0.0976	-0.114	-0.0244	0.0007	-0.1543	-0.0121	-0.15
11	0.0941	-0.2146	0.1844	0.6041	-0.396	0.3666	0.0027	0.1756	0.2029	0.0045	0.1038	0.1043	-0.209	-0.1718	-0.1065	-0.1426	0.0066	0.0196	-0.0864	-0.1257	-0.0909
12	0.2403	-0.176	0.0553	1.0783	-1.4857	2.3218	0.0554	-0.0111	0.0396	0.0057	0.0163	0.1178	-0.112	0.1187	-0.0718	-0.1453	0.0149	0.0079	-0.1034	-0.1008	-0.1002
13	0.327	-0.702	0.4692	1.9714	-0.7712	0.7934	-0.0285	0.1178	0.1437	0.2623	0.4091	0.4687	-0.1919	-0.3462	-0.3806	-0.1444	0.0149	0.0039	-0.0341	-0.1499	-0.1013
14	0.3208	0.1961	-0.3869	0.2424	-0.048	0.7565	-0.1041	0.0828	0.2081	0.1557	-0.2161	-0.32	-0.1177	0.2044	0.3202	-0.1423	-0.009	0.0268	-0.0578	-0.1544	-0.0913
15	0.2052	-0.5317	0.4452	1.5005	-1.2666	1.0699	-0.2317	0.3612	0.4808	-0.0049	-0.1369	-0.1338	-0.5257	0.1776	0.3686	-0.0914	-0.0278	0.0854	-0.1023	-0.0966	-0.098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	21 - 55
2	X-RAY DIFFRACTION	2	A	59 - 105
3	X-RAY DIFFRACTION	3	A	106 - 161
4	X-RAY DIFFRACTION	4	A	167 - 192
5	X-RAY DIFFRACTION	5	A	193 - 197
6	X-RAY DIFFRACTION	6	A	198 - 254
7	X-RAY DIFFRACTION	7	A	255 - 377
8	X-RAY DIFFRACTION	8	A	378 - 448
9	X-RAY DIFFRACTION	9	A	449 - 518
10	X-RAY DIFFRACTION	10	A	519 - 524
11	X-RAY DIFFRACTION	11	A	530 - 581
12	X-RAY DIFFRACTION	12	A	582 - 587
13	X-RAY DIFFRACTION	13	A	588 - 623
14	X-RAY DIFFRACTION	14	A	624 - 638
15	X-RAY DIFFRACTION	15	A	639 - 654

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