PDB-3a2n: Crystal structure of DBJA (Wild Type Type II P21)

ID or keywords:

Entry

Database: PDB / ID: 3a2n

Title

Crystal structure of DBJA (Wild Type Type II P21)

Components

Haloalkane dehalogenase

Keywords

HYDROLASE / A/B-HYDROLASE

Function / homology

Function and homology information

haloalkane dehalogenase / haloalkane dehalogenase activity / hydrolase activity / identical protein binding
Similarity search - Function

Biological species

Bradyrhizobium japonicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Sato, Y. / Senda, T.

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering
Authors: Prokop, Z. / Sato, Y. / Brezovsky, J. / Mozga, T. / Chaloupkova, R. / Koudelakova, T. / Jerabek, P. / Stepankova, V. / Natsume, R. / van Leeuwen, J.G. / Janssen, D.B. / Florian, J. / Nagata, ...

History

Deposition	May 23, 2009	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 26, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3a2n.cif.gz	244.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3a2n.ent.gz	198.6 KB	Display	PDB format
PDBx/mmJSON format	3a2n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3a2n_validation.pdf.gz	464.6 KB	Display	wwPDB validaton report
Full document	3a2n_full_validation.pdf.gz	494.7 KB	Display
Data in XML	3a2n_validation.xml.gz	47.7 KB	Display
Data in CIF	3a2n_validation.cif.gz	68.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a2/3a2n ftp://data.pdbj.org/pub/pdb/validation_reports/a2/3a2n	HTTPS FTP

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Related structure data

Related structure data	3a2lC 3a2mSC 3afiC 3a1o PDB Unreleased entry C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6xy9-d 4i73-2 2r2d-2 4i74-1 2r2d-1 3u1t-d 3ebl-9 6p9u-3 2eiv-2 6p9u-4 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
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Haloalkane dehalogenase

B: Haloalkane dehalogenase

E: Haloalkane dehalogenase

F: Haloalkane dehalogenase

hetero molecules

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

1

A: Haloalkane dehalogenase

B: Haloalkane dehalogenase

hetero molecules

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

2

E: Haloalkane dehalogenase

F: Haloalkane dehalogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	125.534, 47.766, 99.410
Angle α, β, γ (deg.)	90.00, 93.61, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Haloalkane dehalogenase Mass: 34344.109 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Strain: USDA110 / Gene: DBJA / Plasmid: PYBJA3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P59337, haloalkane dehalogenase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	VAL AND ASP WERE ADDED TO C-TERMINUS. THE DBJAWT CONSTRUCT CODES FOR RESIDUES 1-310 OF DBJA WITH C- ...VAL AND ASP WERE ADDED TO C-TERMINUS. THE DBJAWT CONSTRUCT CODES FOR RESIDUES 1-310 OF DBJA WITH C-TERMINUS FUSED TO A RESTRICTION SITE OF SAL I WITH SEQUENCE AVD, WHERE A IS RESIDUE 310 OF THE DBJAWT SEQUENCE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.19 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: PEG 4000, PH 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2006
Radiation	Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.89→50 Å / Num. obs: 94042 / % possible obs: 99.5 % / Observed criterion σ(I): 14.9 / Redundancy: 4.8 % / R_merge(I) obs: 0.063
Reflection shell	Resolution: 1.89→1.96 Å / Redundancy: 3.4 %

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Processing

Software

Name: REFMAC / Version: 5.2.0005 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A2M

3a2m

Resolution: 1.89→32.81 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.932 / SU B: 5.613 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22783	4717	5 %	RANDOM
R_work	0.19151	-	-	-
obs	0.19331	89306	99.29 %	-

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: 28.735 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0.12 Å²
2-	-	-0.02 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→32.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9288	0	3	489	9780

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	9584
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.333	1.951	13055
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.395	5	1193
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.653	21.938	454
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.541	15	1408
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.431	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1388
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7604
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	4774
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	6551
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	603
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	0.239	0.2	131
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.153	0.2	23
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	0.694	1.5	6141
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.096	2	9579
X-RAY DIFFRACTION	r_scbond_it	1.845	3	3890
X-RAY DIFFRACTION	r_scangle_it	2.897	4.5	3476
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.892→1.941 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.224	374	-
R_work	0.18	6326	-
obs	-	-	96.54 %

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	2.094	-0.3817	0.6276	0.6194	-0.3063	1.3282	-0.0649	-0.0102	0.2128	0.0042	-0.0434	-0.0497	-0.1651	-0.1397	0.1083	-0.0492	-0.0081	0.0046	-0.0161	0.0154	-0.0584	12.6225	4.7015	10.951
2	8.8212	-2.1241	-1.5652	2.8965	0.6468	3.7428	-0.296	-0.3402	-1.2338	0.3766	0.279	-0.2527	0.9261	0.0626	0.017	0.1336	-0.0715	-0.0059	-0.1007	0.0249	0.1322	6.0825	-20.3806	14.9031
3	10.4809	0.1288	3.0249	1.0017	-0.2975	8.1633	0.1218	-0.534	-0.3564	0.0225	-0.1719	-0.0291	0.388	-0.5871	0.0501	-0.1142	-0.1537	0.0222	0.1345	0.0503	-0.1148	-5.4108	-9.3387	17.9934
4	2.3434	0.2124	0.3748	0.6354	-0.1751	1.26	0.0472	-0.2074	-0.1969	0.0104	-0.0239	-0.0501	0.1664	-0.188	-0.0232	-0.0596	-0.0398	0.0212	-0.038	0.039	-0.0977	13.8943	-6.7628	15.3078
5	1.1784	-0.0275	0.0116	0.8599	-0.3633	1.1293	0.0275	0.0967	-0.0374	-0.0275	-0.0435	-0.0904	0.1032	0.072	0.016	0.0008	0.0103	0.025	-0.0946	-0.0039	-0.0309	49.0899	-3.6919	30.1528
6	5.2886	-1.9696	2.0111	3.3884	-1.3904	5.3669	-0.0514	-0.4342	0.3121	0.286	0.103	0.2199	-0.5947	-0.436	-0.0516	0.0747	0.0061	0.0495	-0.1136	-0.0461	-0.0199	42.8698	14.736	48.2632
7	8.9939	-0.2183	4.3969	1.453	0.6235	4.599	-0.0578	-0.1936	0.0273	0.2351	0.0125	0.0314	-0.115	0.0433	0.0453	0.0479	-0.0096	0.0203	-0.0602	0.0031	-0.0963	48.7395	0.0993	53.8973
8	1.0863	-0.0284	0.1179	0.5991	-0.3088	1.322	-0.005	-0.0429	0.1087	0.0897	0.0292	0.0136	-0.0827	-0.0867	-0.0243	-0.0115	0.0093	0.0321	-0.1073	-0.0058	-0.0509	41.901	4.5564	35.9628
9	3.737	-1.4769	-1.1497	2.5204	0.5807	3.6615	0.185	0.8795	-0.8554	-0.1675	-0.5237	0.6527	0.1373	-1.3356	0.3387	-0.1992	-0.0044	-0.0529	0.3974	-0.2857	0.0807	14.5761	-0.9999	-31.878
10	3.8745	3.6848	1.8766	7.9236	4.701	9.4451	0.4433	0.768	0.5257	-0.6642	0.031	-1.2701	-1.0755	-0.9272	-0.4743	0.0324	0.3082	0.0666	0.0725	0.0562	0.0062	21.8264	17.991	-48.5633
11	45.8756	-4.9862	14.8698	3.5504	14.3465	89.518	-0.4406	0.9609	2.0832	0.0388	-0.0707	0.1242	-0.2477	0.0965	0.5113	0.078	0.0322	-0.0496	0.0243	-0.0649	-0.0042	16.2933	3.6846	-55.1559
12	2.915	-1.0882	-0.7732	0.9004	0.7352	2.814	0.4004	0.7871	-0.0927	-0.2507	-0.401	0.0836	-0.2927	-0.7843	0.0006	-0.0102	0.1921	0.002	0.2922	-0.0577	-0.111	22.1481	7.3928	-36.7704
13	1.3297	0.1094	0.104	0.4916	0.4118	0.6051	-0.0229	-0.0069	0.0913	-0.0351	-0.0143	0.0098	-0.0784	-0.0329	0.0372	0.0133	-0.0016	0.0159	-0.0747	0.0018	-0.0293	50.6705	4.7336	-11.0786
14	6.5957	2.4887	1.8983	2.9031	0.8855	1.3598	0.0766	0.2221	-0.6429	-0.0792	0.0312	-0.0815	0.2404	0.1092	-0.1078	0.0581	0.0043	0.0355	-0.1488	-0.0304	0.0492	54.8989	-20.7211	-14.7964
15	4.4949	-0.9036	2.4786	0.8377	0.6371	4.007	0.1058	0.1522	-0.2575	-0.0408	0.0015	0.0248	0.1707	0.1299	-0.1073	0.0022	0.0177	0.0365	-0.0654	-0.0275	-0.0089	67.5832	-10.86	-17.5354
16	1.3581	-0.3397	0.043	0.6161	0.1951	0.7533	-0.0021	0.1249	-0.1555	-0.0154	-0.0216	0.0478	0.0591	-0.026	0.0237	-0.013	-0.0132	0.0248	-0.0854	-0.0198	-0.0458	48.566	-6.5638	-15.4452

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 134
2	X-RAY DIFFRACTION	2	A	135 - 163
3	X-RAY DIFFRACTION	3	A	164 - 180
4	X-RAY DIFFRACTION	4	A	181 - 300
5	X-RAY DIFFRACTION	5	B	10 - 134
6	X-RAY DIFFRACTION	6	B	135 - 163
7	X-RAY DIFFRACTION	7	B	164 - 180
8	X-RAY DIFFRACTION	8	B	181 - 300
9	X-RAY DIFFRACTION	9	E	10 - 134
10	X-RAY DIFFRACTION	10	E	135 - 163
11	X-RAY DIFFRACTION	11	E	164 - 180
12	X-RAY DIFFRACTION	12	E	181 - 300
13	X-RAY DIFFRACTION	13	F	10 - 134
14	X-RAY DIFFRACTION	14	F	135 - 163
15	X-RAY DIFFRACTION	15	F	164 - 180
16	X-RAY DIFFRACTION	16	F	181 - 300

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