PDB-1vz5: Succinate Complex of AtsK

ID or keywords:

Entry

Database: PDB / ID: 1vz5

Title

Succinate Complex of AtsK

Components

PUTATIVE ALKYLSULFATASE ATSK

Keywords

OXIDOREDUCTASE / NON-HEME FE(II) ALPHAKETOGLUTARATE DEPENDENT DIOXYGENASE / ALKYLSULFATASE / JELLY ROLL / SULFATASE / SELF HYDROXYLATION

Function / homology

Function and homology information

alkyl sulfatase / 2-oxoglutarate-dependent dioxygenase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

PSEUDOMONAS PUTIDA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Mueller, I. / Stueckl, A.C. / Uson, I. / Kertesz, M.

Citation

Journal: J.Biol.Chem. / Year: 2005
Title: Succinate Complex Crystal Structures of the Alpha-Ketoglutarate-Dependent Dioxygenase Atsk: Steric Aspects of Enzyme Self-Hydroxylation
Authors: Mueller, I. / Stueckl, A.C. / Wakeley, J. / Kertesz, M. / Uson, I.

History

Deposition	May 14, 2004	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 15, 2004	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	1vz5.cif.gz	211 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	1vz5_validation.pdf.gz	459.9 KB	Display	wwPDB validaton report
Full document	1vz5_full_validation.pdf.gz	470.7 KB	Display
Data in XML	1vz5_validation.xml.gz	42.2 KB	Display
Data in CIF	1vz5_validation.cif.gz	60.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/1vz5 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vz5	HTTPS FTP

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Related structure data

Related structure data	1vz4C 1oihS 1oii 1oij 1oik S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1vz4-1 3r1j-1 1oik-1 4ffa-d 1oih-d 5keu-2 3cpi-d 6d0o-d 4j5i-2 4cvy-d 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

Deposited unit

A: PUTATIVE ALKYLSULFATASE ATSK

B: PUTATIVE ALKYLSULFATASE ATSK

C: PUTATIVE ALKYLSULFATASE ATSK

D: PUTATIVE ALKYLSULFATASE ATSK

hetero molecules

133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	72.514, 145.815, 158.788
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	13 - 80
2	1	1	2	B	13 - 80
3	1	1	2	C	13 - 80
4	1	1	2	D	13 - 80
1	2	1	2	A	103 - 165
2	2	1	2	B	103 - 165
3	2	1	2	C	103 - 165
4	2	1	2	D	103 - 165
1	3	1	2	A	191 - 299
2	3	1	2	B	191 - 299
3	3	1	2	C	191 - 299
4	3	1	2	D	191 - 299

#1: Protein	PUTATIVE ALKYLSULFATASE ATSK Mass: 33248.402 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ATSK-SUCCINATE COMPLEX / Source: (natural) PSEUDOMONAS PUTIDA (bacteria) / Strain: S-313 / References: UniProt: Q9WWU5
#2: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 524 / 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: 3.16 Å³/Da / Density % sol: 60 % Description: SIDE CHAINS IN ACTIVE SITE TRUNCATED FOR MOLECULAR REPLACEMENT MODEL
Crystal grow	pH: 7 Details: 25 MM AMMONIUM SULFATE 175 MM SODUIM SUCCINATE PH 5.6, 15 % PEG 4000 30 % GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. obs: 92306 / % possible obs: 100 % / Redundancy: 6 % / R_merge(I) obs: 0.127 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.15→2.25 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.522 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0003	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OIH

1oih

Resolution: 2.15→48.8 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.932 / SU B: 3.906 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	4734	5.1 %	RANDOM
R_work	0.194	-	-	-
obs	0.196	87475	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 26.58 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.47 Å²	0 Å²	0 Å²
2-	-	0.86 Å²	0 Å²
3-	-	-	0.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→48.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7591	0	32	524	8147

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.027	0.021	7789
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.963	1.919	10633
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.877	5	980
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.301	22.857	350
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.361	15	1124
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.41	15	67
X-RAY DIFFRACTION	r_chiral_restr	0.157	0.2	1224
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	5995
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	3262
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	5186
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.229	0.2	22
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.109	0.2	7
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	2.096	2	5097
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.148	4	7887
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.375	4	3147
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.954	6	2746
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

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	932	tight positional	0.07	0.05
2	B	932	tight positional	0.07	0.05
3	C	932	tight positional	0.07	0.05
4	D	932	tight positional	0.09	0.05
1	A	818	medium positional	0.21	0.5
2	B	818	medium positional	0.27	0.5
3	C	818	medium positional	0.25	0.5
4	D	818	medium positional	0.27	0.5
1	A	932	tight thermal	0.41	0.5
2	B	932	tight thermal	0.45	0.5
3	C	932	tight thermal	0.35	0.5
4	D	932	tight thermal	0.53	0.5
1	A	818	medium thermal	1.81	2
2	B	818	medium thermal	2.06	2
3	C	818	medium thermal	1.87	2
4	D	818	medium thermal	2.29	2

LS refinement shell

Resolution: 2.15→2.21 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.276	615	-
R_work	0.223	6131	-
obs	-	-	99.99 %

Refinement TLS params.

Method: refined / 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)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4562	-0.0599	-0.1313	0.8506	0.2118	0.0827	0.0403	-0.0384	-0.081	0.0907	-0.0071	-0.0499	-0.0166	0.0006	-0.0333	0.0518	0.0008	-0.0312	0.0085	-0.0099	0.053	56.177	121.53	30.33
2	0.3424	0.1518	0.144	0.8921	0.1382	0.0673	0.0284	0.0294	0.0753	-0.0895	-0.0078	-0.0215	0.0289	-0.0034	-0.0205	0.0394	0.0009	0.0248	0.015	-0.0108	0.054	55.317	167.663	50.323
3	0.4513	-0.1382	0.0891	0.176	0.234	1.1181	0.0509	-0.115	-0.0476	0.0269	-0.0378	0.0259	0.1272	-0.1578	-0.013	0.0669	-0.0407	0.0207	0.0696	-0.0067	0.0387	34.01	148.432	63.685
4	1.2679	-0.0089	-0.3943	0.2714	0.1393	1.1249	0.1555	0.3284	0.1115	-0.0351	-0.0696	0.0015	-0.1542	-0.2206	-0.0858	0.0718	0.0801	0.0056	0.1178	0.0288	0.0182	35.853	140.734	15.24

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 300
2	X-RAY DIFFRACTION	2	B	13 - 300
3	X-RAY DIFFRACTION	3	C	13 - 299
4	X-RAY DIFFRACTION	4	D	13 - 299

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