PDB-3u1t: Haloalkane Dehalogenase, DmmA, of marine microbial origin

ID or keywords:

Entry

Database: PDB / ID: 3u1t

Title

Haloalkane Dehalogenase, DmmA, of marine microbial origin

Components

DmmA Haloalkane Dehalogenase

Keywords

HYDROLASE / alpha/beta-hydrolase / Haloalkane Dehalogenase

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Gehret, J.J. / Smith, J.L.

Citation

Journal: Protein Sci. / Year: 2012
Title: Structure and activity of DmmA, a marine haloalkane dehalogenase.
Authors: Gehret, J.J. / Gu, L. / Geders, T.W. / Brown, W.C. / Gerwick, L. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L.

History

Deposition	Sep 30, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Apr 18, 2012	Group: Database references
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	Nov 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	3u1t.cif.gz	262.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3u1t.ent.gz	213.6 KB	Display	PDB format
PDBx/mmJSON format	3u1t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3u1t_validation.pdf.gz	438.3 KB	Display	wwPDB validaton report
Full document	3u1t_full_validation.pdf.gz	439.2 KB	Display
Data in XML	3u1t_validation.xml.gz	31.2 KB	Display
Data in CIF	3u1t_validation.cif.gz	44.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u1/3u1t ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u1t	HTTPS FTP

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Related structure data

Similar structure data	3h1b-d 1g42-d 6y9f-d 5lu9-d 6s06-d 2qvb-1 6u32-d 6wf7-1 1k63-d 6qro-3 Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (3) #220 - Apr 2018 Dehalogenases similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: DmmA Haloalkane Dehalogenase

B: DmmA Haloalkane Dehalogenase

hetero molecules

69.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DmmA Haloalkane Dehalogenase

hetero molecules

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

2

B: DmmA Haloalkane Dehalogenase

hetero molecules

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

3

A: DmmA Haloalkane Dehalogenase

B: DmmA Haloalkane Dehalogenase

hetero molecules

A: DmmA Haloalkane Dehalogenase

B: DmmA Haloalkane Dehalogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.784, 99.784, 122.004
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

#1: Protein	DmmA Haloalkane Dehalogenase Mass: 34715.668 Da / Num. of mol.: 2 / Fragment: DmmAshort Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Plasmid: pET-24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DND9, haloalkane dehalogenase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	SQUENCE WAS ORIGINALLY ANNOTATED AS CURN FROM CYANOBACTERIA LYNGBYA MAJUSCULA. IT IS NOW THOUGHT ...SQUENCE WAS ORIGINALLY ANNOTATED AS CURN FROM CYANOBACTERIA LYNGBYA MAJUSCULA. IT IS NOW THOUGHT THAT CURN GENETIC MATERIAL IS FROM A BACTERIA THAT WAS GROWING IN ASSOCIATION WITH L. MAJUSCULA AT THE TIME OF COSMID PREPARATION. CURN HAS BEEN RENAMED DMMA.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2 M sodium malonate pH 7.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97939 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2007 / Details: mirrors

Radiation

Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97939 Å / Relative weight: 1

Reflection

Redundancy: 5.8 % / Av σ(I) over netI: 13.22 / Number: 399056 / R_merge(I) obs: 0.122 / Χ²: 1.02 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 69098 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.74	50	100	1	0.047	1.01	5.9
3.76	4.74	100	1	0.068	1.011	5.9
3.29	3.76	100	1	0.076	1.05	5.9
2.99	3.29	100	1	0.118	1.011	5.9
2.77	2.99	100	1	0.175	1.011	5.9
2.61	2.77	100	1	0.235	1.012	5.8
2.48	2.61	100	1	0.305	1.001	5.8
2.37	2.48	100	1	0.395	1.018	5.8
2.28	2.37	100	1	0.479	1.028	5.6
2.2	2.28	99.9	1	0.548	1.071	5.2

Reflection

Resolution: 2.2→50 Å / Num. obs: 35045 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / R_merge(I) obs: 0.122 / Net I/σ(I): 8.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.2-2.28	5.2	0.549	1	99.9
2.28-2.37	5.6	0.479	1	100
2.37-2.48	5.8	0.395	1	100
2.48-2.61	5.8	0.305	1	100
2.61-2.77	5.8	0.235	1	100
2.77-2.99	5.9	0.175	1	100
2.99-3.29	5.9	0.118	1	100
3.29-3.76	5.9	0.076	1	100
3.76-4.74	5.9	0.068	1	100
4.74-50	5.9	0.047	1	100

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Phasing

Phasing

Method:

SAD

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	26.293	0.086	0.255	0.333	0.356
2	Se	30.358	0.633	0.31	0.103	0.346
3	Se	35.382	0.169	0.172	0.027	0.443
4	Se	20.601	0.687	0.413	0.128	0.306
5	Se	28.886	0.26	0.426	0.224	0.269
6	Se	28.932	0.151	0.387	0.221	0.284
7	Se	32.014	0.682	0.442	0.284	0.332
8	Se	18.977	0.933	0.13	0.242	0.283
9	Se	27.354	0.627	0.253	0.221	0.31
10	Se	25.701	0.243	0.379	0.237	0.262
11	Se	32.629	0.108	0.253	0.179	0.223
12	Se	60	0.894	0.092	0.171	0.244
13	Se	15.99	0.143	0.477	0.143	0.128
14	Se	40.119	0.196	0.48	0.24	0.266
15	Se	30.948	0.943	0.254	0.269	0.208
16	Se	37.548	0.766	0.325	0.189	0.219
17	Se	55.057	0.672	0.399	0.301	0.276
18	Se	17.537	0.09	0.208	0.014	0.113
19	Se	18.819	0.609	0.201	0.111	0.112
20	Se	25.831	0.123	0.423	0.315	0.169
21	Se	56.461	0.053	0.208	0.146	0.233
22	Se	60	0.615	0.207	0.292	0.253

Phasing dm

FOM : 0.68 / FOM acentric: 0.68 / FOM centric: 0.61 / Reflection: 34734 / Reflection acentric: 33845 / Reflection centric: 889

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
6.3-49.9	0.91	0.93	0.73	1532	1419	113
3.9-6.3	0.92	0.92	0.8	4673	4494	179
3.1-3.9	0.86	0.86	0.75	5852	5692	160
2.8-3.1	0.74	0.74	0.62	5866	5735	131
2.4-2.8	0.57	0.58	0.43	10441	10240	201
2.2-2.4	0.41	0.42	0.29	6370	6265	105

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.1	phasing
RESOLVE	2.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
Blu-Ice	epics	data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.2→86.39 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.24 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1995 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17728	1746	5 %	RANDOM
R_work	0.13882	-	-	-
obs	0.14079	33173	99.62 %	-
all	-	37919	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.696 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.1 Å²	0.55 Å²	0 Å²
2-	-	1.1 Å²	0 Å²
3-	-	-	-1.66 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→86.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4628	0	18	497	5143

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	4801
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.195	1.973	6556
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.974	5	603
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.819	23.395	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.124	15	729
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.544	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	705
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.022	3777
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.362	1.5	3003
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.718	2	4848
X-RAY DIFFRACTION	r_scbond_it	1.479	3	1798
X-RAY DIFFRACTION	r_scangle_it	2.369	4.5	1704
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.198→2.255 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.249	130	-
R_work	0.182	2408	-
obs	-	-	97.69 %

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	1.4868	0.375	-0.3495	0.536	-0.5319	1.1181	-0.0018	0.1047	-0.0084	-0.0696	-0.0127	0.0334	0.0493	-0.0194	0.0145	0.067	-0.0087	0.0054	0.1005	-0.0148	0.024	46.6973	23.6756	50.2337
2	0.9853	0.2497	-0.2853	0.7046	0.164	1.1528	0.0185	0.045	0.0871	0.0606	-0.0568	0.0122	-0.2264	0.0197	0.0383	0.0806	-0.0111	0.0115	0.076	0.0054	0.0641	46.9589	33.7999	59.9725
3	0.7738	-0.0607	0.1786	0.6435	0.1995	1.4357	0.0217	0.0537	-0.053	0.0567	-0.0529	-0.0577	-0.029	0.1202	0.0312	0.0347	-0.0282	0.015	0.1314	0.0239	0.0488	63.5302	22.6696	64.0506
4	15.2278	0.2964	-2.7779	2.2439	1.3074	2.0057	0.1226	-0.1837	0.3421	0.2074	-0.1326	0.0428	-0.22	-0.0686	0.0099	0.1938	-0.0246	-0.0013	0.0422	-0.0396	0.0779	48.9805	38.3874	70.2081
5	1.4247	0.301	-0.0075	0.9816	-0.1163	0.8556	0.0574	-0.0433	0.0631	0.0819	-0.0648	0.0636	0.0037	-0.0594	0.0074	0.0603	-0.0187	0.0289	0.0876	-0.023	0.0378	38.7606	21.518	68.3103
6	0.3806	-0.1713	-0.1389	1.5435	-0.6606	1.3494	0.0351	-0.1	0.0199	0.249	-0.028	0.1529	-0.0265	-0.0838	-0.0071	0.0667	-0.0487	0.0466	0.1125	-0.0616	0.0518	23.9821	1.3443	86.7254
7	0.5018	-0.1122	-0.0885	1.1225	-0.3363	1.413	0.0782	-0.0821	-0.0203	-0.0374	-0.0276	0.3102	-0.0515	-0.2581	-0.0506	0.0328	-0.0361	0.0194	0.1528	-0.0648	0.141	14.9855	4.511	77.4791
8	17.7836	-6.6739	-0.0033	4.2399	-5.7763	19.265	1.0609	0.8466	0.7152	-0.3391	-0.9366	-0.2451	-0.3869	1.655	-0.1243	0.4719	0.0174	-0.0082	0.3442	-0.1097	0.163	21.1927	-13.4015	62.1826
9	0.1288	-0.0664	-0.2973	2.4588	0.151	0.8922	-0.023	-0.019	-0.0446	-0.0585	-0.0529	0.0209	0.2113	0.0023	0.0759	0.1207	-0.0411	-0.0016	0.0904	-0.0399	0.0572	27.7442	-14.2107	77.7459
10	1.1022	0.4081	-0.2505	2.305	-0.3365	0.9864	0.0932	0.0596	0.0381	-0.2272	-0.0986	0.1901	-0.008	-0.0652	0.0053	0.0438	0.0031	-0.0098	0.0976	-0.0523	0.0383	23.0585	7.5968	68.5527

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	44 - 113
2	X-RAY DIFFRACTION	2	A	114 - 177
3	X-RAY DIFFRACTION	3	A	178 - 256
4	X-RAY DIFFRACTION	4	A	257 - 273
5	X-RAY DIFFRACTION	5	A	274 - 341
6	X-RAY DIFFRACTION	6	B	44 - 118
7	X-RAY DIFFRACTION	7	B	119 - 176
8	X-RAY DIFFRACTION	8	B	177 - 196
9	X-RAY DIFFRACTION	9	B	197 - 251
10	X-RAY DIFFRACTION	10	B	252 - 341

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