PDB-3bjx: Structure of a Group I haloacid dehalogenase from Pseudomonas put...

ID or keywords:

Entry

Database: PDB / ID: 3bjx

Title

Structure of a Group I haloacid dehalogenase from Pseudomonas putida strain PP3

Components

Halocarboxylic acid dehalogenase DehI

Keywords

HYDROLASE /

Plasmid

Function / homology

2-haloacid dehalogenase, DehI / Halocarboxylic acid dehydrogenase DehI / hydrolase activity, acting on acid halide bonds, in C-halide compounds / Halocarboxylic acid dehalogenase DehI

Function and homology information

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Schmidberger, J.W. / Wilce, M.C.J.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: The crystal structure of DehI reveals a new alpha-haloacid dehalogenase fold and active-site mechanism
Authors: Schmidberger, J.W. / Wilce, J.A. / Weightman, A.J. / Whisstock, J.C. / Wilce, M.C.J.

History

Deposition	Dec 5, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Remark 40

MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjx ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjx	HTTPS FTP

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Related structure data

Similar structure data	5v9h-1 3sqc-1 5v95-d 4ywb-2 6g8f-d 5v9h-2 3sqc-3 3avs-d 3sqc-2 1sqc-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Halocarboxylic acid dehalogenase DehI

B: Halocarboxylic acid dehalogenase DehI

C: Halocarboxylic acid dehalogenase DehI

D: Halocarboxylic acid dehalogenase DehI

hetero molecules

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

1

A: Halocarboxylic acid dehalogenase DehI

B: Halocarboxylic acid dehalogenase DehI

hetero molecules

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

2

C: Halocarboxylic acid dehalogenase DehI

D: Halocarboxylic acid dehalogenase DehI

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.323, 111.864, 75.181
Angle α, β, γ (deg.)	90.000, 93.710, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Halocarboxylic acid dehalogenase DehI Mass: 34866.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: PP3 / Gene: dehI / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: Q8GJ84, (S)-2-haloacid dehalogenase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE PUBLISHED SEQUENCE FOR DEHI WITH ASSESSION CODE Q8GJ84 IS WRONG FOR RESIDUE 229. A PROLINE IS ...THE PUBLISHED SEQUENCE FOR DEHI WITH ASSESSION CODE Q8GJ84 IS WRONG FOR RESIDUE 229. A PROLINE IS REPORTED FOR THIS RESIDUE BUT IS IN FACT AN ARGININE AS REPORTED IN THIS STRUCTURE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 40.17 %
Crystal grow	Temperature: 298 K / Method: hanging drop / pH: 6 Details: 25% PEG 3350 w/v, 0.4M Li2SO4, 0.1M Bis-Tris pH 6.0, hanging drop, temperature 298K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength	Wavelength (Å)
ROTATING ANODE			RIGAKU	1	1.5418	1.5418
SYNCHROTRON	SSRL	BL9-1		2		0.97929, 0.97925, 0.91837

Detector

Type	ID	Detector	Date	Details
RIGAKU RAXIS	1	IMAGE PLATE	Feb 20, 2006	Mirrors
ADSC QUANTUM 315	2	CCD	Feb 20, 2006	Vertical focusing mirror

Radiation

ID	Protocol	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	x-ray	1
2	MAD	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	0.97929	1
3	0.97925	1
4	0.91837	1

Reflection

Resolution: 2.3→75.024 Å / Num. obs: 48240 / % possible obs: 96.3 % / Redundancy: 2.5 % / R_merge(I) obs: 0.118 / R_sym value: 0.118 / Net I/σ(I): 6.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.3-2.42	2	0.454	1.6	11547	5900	0.454	81
2.42-2.57	2.5	0.409	1.8	16896	6847	0.409	99.1
2.57-2.75	2.5	0.322	2.3	16376	6462	0.322	99.8
2.75-2.97	2.6	0.232	3.2	15435	6045	0.232	99.7
2.97-3.25	2.6	0.165	4.5	14186	5520	0.165	99.4
3.25-3.64	2.6	0.101	7.3	12923	4997	0.101	99.2
3.64-4.2	2.6	0.064	10.8	11453	4392	0.064	98.8
4.2-5.14	2.6	0.046	15.2	9749	3706	0.046	98.3
5.14-7.27	2.7	0.054	13.4	7538	2838	0.054	97.1
7.27-44.81	2.7	0.03	19.3	4071	1533	0.03	93.8

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.979	3.47	-10.63
1	3 wavelength	2	0.918	3.4	-1.8
1	3 wavelength	3	0.979	5.72	-8.22

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	44.43	0.911	0.315	0.651	0.667
2	Se	35.346	0.676	0.357	0.932	0.55
3	Se	20.395	0.468	0.403	0.076	0.558
4	Se	33.162	0.907	0.135	0.337	0.498
5	Se	30.877	0.084	0.269	0.481	0.612
6	Se	26.527	0.512	0.484	0.087	0.476
7	Se	39.123	0.629	0.483	0.018	0.49
8	Se	58.075	0.026	0.126	0.662	0.595
9	Se	29.55	0.094	0.188	0.517	0.523
10	Se	60	0.674	0.545	0.04	0.677
11	Se	51.539	0.004	0.19	0.619	0.636
12	Se	60	0.911	0.333	0.414	0.735
13	Se	60	0.778	0.139	0.903	0.585
14	Se	52.062	0.127	0.426	0.743	0.522
15	Se	60	0.322	0.34	0.995	0.621
16	Se	60	0.009	0.332	0.336	0.549
17	Se	54.978	0.332	0.536	0.901	0.589
18	Se	60	0.696	0.454	0.904	0.429
19	Se	60	0.412	0.341	0.915	0.522
20	Se	60	0.329	0.341	0.892	0.55
21	Se	60	0.872	0.535	0.746	0.55
22	Se	60	0.867	0.23	0.327	0.371
23	Se	60	0.894	0.328	0.341	0.472
24	Se	45.788	0.99	0.264	0.38	0.529
25	Se	48.007	0.755	0.247	0.138	0.493
26	Se	51.155	0.364	0.408	0.983	0.568
27	Se	47.322	0.315	0.438	0.864	0.377
28	Se	60	0.877	0.213	0.673	0.496
29	Se	60	0.921	0.124	0.622	0.559
30	Se	1	0.009	0.499	0.963	0.002
31	Se	60	0.636	0.545	0.951	0.451

Phasing dm

FOM : 0.65 / FOM acentric: 0.66 / FOM centric: 0.6 / Reflection: 27694 / Reflection acentric: 26674 / Reflection centric: 1020

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8-74.682	0.94	0.94	0.86	1229	1106	123
5-8	0.86	0.87	0.74	3709	3515	194
4-5	0.85	0.86	0.68	4633	4454	179
3.5-4	0.77	0.77	0.69	4695	4539	156
3-3.5	0.56	0.56	0.46	8311	8080	231
2.8-3	0.31	0.31	0.17	5117	4980	137

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
SOLVE	2.12	phasing
RESOLVE	2.12	phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
CrystalClear		data collection

Refinement

Method to determine structure:

MAD / Resolution: 2.3→38.15 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.896 / SU B: 7.727 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.559 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25018	2457	5.1 %	RANDOM
R_work	0.18117	-	-	-
obs	0.18463	45759	96.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.182 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	-0.06 Å²
2-	-	-0.06 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→38.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9435	0	80	449	9964

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	9717
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.447	1.99	13219
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.219	5	1207
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.176	22.926	417
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.329	15	1611
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.57	15	86
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1479
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7344
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	4876
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	6680
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.17	0.2	564
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	0.217	0.2	114
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.176	0.2	25
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	1.482	2	6233
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.215	3	9759
X-RAY DIFFRACTION	r_scbond_it	1.52	2	3922
X-RAY DIFFRACTION	r_scangle_it	2.234	3	3460
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.36	141	-
R_work	0.23	2676	-
obs	-	-	76.01 %

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