PDB-3kg7: Dehydratase domain from CurH module of Curacin polyketide synthase

ID or keywords:

Entry

Database: PDB / ID: 3kg7

Title

Dehydratase domain from CurH module of Curacin polyketide synthase

Components

CurH

Keywords

LYASE /

polyketide synthase / double hotdog fold /

dehydratase

Function / homology

Function and homology information

phosphopantetheine binding /

transferase activity /

oxidoreductase activity / identical protein binding
Similarity search - Function

Biological species

Lyngbya majuscula (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.77 Å

Authors

Akey, D.L. / Smith, J.L.

Citation

Journal: Structure / Year: 2010
Title: Crystal Structures of Dehydratase Domains from the Curacin Polyketide Biosynthetic Pathway.
Authors: Akey, D.L. / Razelun, J.R. / Tehranisa, J. / Sherman, D.H. / Gerwick, W.H. / Smith, J.L.

History

Deposition	Oct 28, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kg7.cif.gz	227.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3kg7.ent.gz	193.5 KB	Display	PDB format
PDBx/mmJSON format	3kg7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kg/3kg7 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/3kg7	HTTPS FTP

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Related structure data

Related structure data	3kg6C 3kg8C 3kg9C C: citing same article (ref.)
Similar structure data	5mlx-d 4bym-d 5tz6-d 4huo-2 5o15-d 3kg8-d 4hup-2 5bkb-1 5il5-1 2vc3-1 5mly-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) 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

Related structure data

3kg6C

3kg8C

3kg9C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (13) #13 - Jan 2001 Alcohol Dehydrogenase similarity (5) #239 - Nov 2019 Phospholipase A2 similarity (1) #32 - Aug 2002 Chaperones similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: CurH

B: CurH

C: CurH

D: CurH

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

1

A: CurH

C: CurH

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

2

B: CurH

D: CurH

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

3

A: CurH

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

4

B: CurH

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

5

C: CurH

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

6

D: CurH

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

Unit cell

Length a, b, c (Å)	82.163, 74.447, 103.482
Angle α, β, γ (deg.)	90.00, 108.84, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	B	930 - 1038
2	1	1	2	A	930 - 1038
1	2	1	2	B	1045 - 1055
2	2	1	2	A	1045 - 1055
1	3	1	2	B	1080 - 1141
2	3	1	2	A	1080 - 1141
1	4	1	2	B	1153 - 1184
2	4	1	2	A	1153 - 1184
1	5	1	2	B	1191 - 1225
2	5	1	2	A	1191 - 1225
1	1	2	2	C	930 - 1038
2	1	2	2	A	930 - 1038
1	2	2	2	C	1045 - 1055
2	2	2	2	A	1045 - 1055
1	3	2	2	C	1080 - 1141
2	3	2	2	A	1080 - 1141
1	4	2	2	C	1153 - 1184
2	4	2	2	A	1153 - 1184
1	5	2	2	C	1191 - 1225
2	5	2	2	A	1191 - 1225
1	1	3	2	D	930 - 1038
2	1	3	2	A	930 - 1038
1	2	3	2	D	1045 - 1055
2	2	3	2	A	1045 - 1055
1	3	3	2	D	1080 - 1141
2	3	3	2	A	1080 - 1141
1	4	3	2	D	1153 - 1184
2	4	3	2	A	1153 - 1184
1	5	3	2	D	1191 - 1225
2	5	3	2	A	1191 - 1225

NCS ensembles :

ID
1
2
3

#1: Protein	CurH Mass: 32948.219 Da / Num. of mol.: 4 / Fragment: Dehydratase domain, residues 934-1233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lyngbya majuscula (bacteria) / Gene: curH / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNE5, EC: 4.2.1.61
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

CurH

Mass: 32948.219 Da / Num. of mol.: 4 / Fragment: Dehydratase domain, residues 934-1233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Lyngbya majuscula (bacteria) / Gene: curH / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNE5, EC: 4.2.1.61

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.27 Å³/Da / Density % sol: 45.88 %
Crystal grow	Temperature: 293 K / pH: 6.5 Details: 15% PEG 4000, 10% PEG 400, 2 mM DTT, 100 mM bis-Tris propane pH 6.5, 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: 0.97945, 0.97962

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: MIRRORS

Radiation

Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97945	1
2	0.97962	1

Reflection

Redundancy: 3.9 % / Av σ(I) over netI: 19.67 / Number: 228164 / R_merge(I) obs: 0.091 / Χ²: 1.1 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 58230 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.03	50	99.6	1	0.056	0.944	3.9
4.79	6.03	100	1	0.07	1.053	4
4.18	4.79	99.9	1	0.074	1.076	3.9
3.8	4.18	100	1	0.084	0.991	3.9
3.53	3.8	99.8	1	0.119	1.027	3.8
3.32	3.53	100	1	0.162	1.049	3.9
3.15	3.32	100	1	0.233	1.077	3.9
3.02	3.15	100	1	0.356	1.163	3.9
2.9	3.02	100	1	0.568	1.31	3.9
2.8	2.9	100	1	0.784	1.316	3.9

Reflection

Resolution: 2.77→50 Å / Num. obs: 29940 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / B_iso Wilson estimate: 80.8 Å² / R_merge(I) obs: 0.107 / R_sym value: 0.107 / Net I/σ(I): 19.7

Reflection shell

Resolution: 2.8→2.91 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.813 / Mean I/σ(I) obs: 2.7 / R_sym value: 0.813 / % possible all: 100

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE		phasing
RESOLVE		phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.77→48.97 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 39.651 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.269	1996	6.7 %	RANDOM
R_work	0.203	-	-	-
obs	0.208	29844	98.8 %	-
all	-	29844	-	-

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: 85.24 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.68 Å²	0 Å²	0.41 Å²
2-	-	5.39 Å²	0 Å²
3-	-	-	-3.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.77→48.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9031	0	0	45	9076

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	9267
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.085	1.958	12668
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.482	5	1139
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.868	24.6	437
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.537	15	1472
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.187	15	52
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	1429
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	7164
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	3807
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	6243
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.129	0.2	301
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	0.177	0.2	54
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.087	0.2	9
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	1.678	5	5890
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.52	7	9362
X-RAY DIFFRACTION	r_scbond_it	1.838	5	3818
X-RAY DIFFRACTION	r_scangle_it	2.532	7	3306
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	B	952	tight positional	0.03	0.05
2	C	956	tight positional	0.04	0.05
3	D	952	tight positional	0.04	0.05
1	B	938	medium positional	0.41	0.5
2	C	941	medium positional	0.55	0.5
3	D	938	medium positional	0.46	0.5
1	B	952	tight thermal	0.08	0.5
2	C	956	tight thermal	0.07	0.5
3	D	952	tight thermal	0.07	0.5
1	B	938	medium thermal	0.52	2
2	C	941	medium thermal	0.55	2
3	D	938	medium thermal	0.62	2

LS refinement shell

Resolution: 2.77→2.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.351	116	-
R_work	0.274	1801	-
obs	-	-	87.37 %

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	4.1741	-1.0019	-3.2427	5.1833	-0.325	8.0765	0.2119	0.0535	0.019	-0.0728	-0.0258	-0.2942	-0.2652	0.3177	-0.1861	-0.2552	-0.0302	-0.0841	-0.4585	0.0351	-0.239	37.476	34.241	48.569
2	4.3016	-1.0071	-1.8481	3.0694	-0.7615	5.6206	0.0571	-0.7613	0.0254	0.6369	0.1334	-0.1214	-0.3051	0.3288	-0.1906	0.0162	0.078	0.0046	-0.2065	0.0962	-0.2926	29.39	32.499	68.289
3	2.564	0.4957	0.6663	4.1243	-1.3667	7.5034	0.5516	-0.0846	0.783	0.4036	0.0717	0.2516	-1.4494	-0.4758	-0.6233	0.1468	0.138	0.2252	-0.3479	0.0223	-0.1331	24.858	44.921	61.31
4	8.6854	-2.0817	-3.2591	8.2552	-2.5208	5.2506	-0.6355	-1.3028	-0.6868	1.1255	0.5132	0.5073	0.8056	0.6511	0.1223	-0.0067	-0.0406	-0.1831	-0.1726	0.2229	-0.2366	26.304	19.662	73.129
5	3.2303	-0.1969	-1.0307	3.3986	-0.8868	9.5127	0.0211	-0.5729	0.1306	0.2841	-0.1488	-0.0626	-0.3311	0.9805	0.1276	-0.4157	-0.0348	0.0609	-0.0782	0.0778	-0.2313	70.55	-0.225	6.96
6	4.2869	0.2143	-1.2439	3.3223	-0.7717	5.9133	0.097	-0.188	-0.0007	-0.4124	-0.1381	-0.2447	-0.1062	1.0755	0.041	-0.2273	0.04	0.0418	-0.115	0.1445	-0.2481	75.218	0.708	-13.944
7	3.3333	1.0318	-0.1443	2.0897	-3.1952	11.8168	-0.2249	-0.1296	-0.4282	-0.2534	-0.1738	-0.3507	1.2924	1.957	0.3987	-0.2874	0.3464	0.1812	0.146	0.1306	-0.1156	81.209	-11.247	-7.209
8	6.4955	-0.9162	2.3058	4.4869	0.4829	11.0533	0.0023	0.5687	-0.3243	-0.7424	-0.5567	-0.0983	-0.6745	-0.47	0.5543	-0.0395	-0.0646	-0.0096	-0.5288	0.2462	-0.0935	66.143	6.127	-22.709
9	4.9191	4.0201	0.193	6.1879	0.7844	6.3915	0.0431	0.284	-0.6928	0.2961	0.1163	-0.4525	0.3435	-0.2394	-0.1594	-0.3882	0.0411	0.0537	-0.3233	-0.099	-0.1508	44.846	35.708	26.91
10	4.087	1.1917	-0.2333	5.5782	0.5003	4.764	-0.6065	1.0675	-0.5819	-1.379	0.7619	-0.9108	0.1168	0.4593	-0.1554	0.0353	-0.3082	0.3434	0.3381	-0.2907	-0.0976	50.795	38.742	6.367
11	10.8229	2.1958	-2.8297	5.3805	0.3403	2.9141	-0.6173	1.5469	-1.2352	-1.3561	1.1147	-0.3958	0.583	-0.5275	-0.4974	0.2069	-0.3521	0.1639	0.2117	-0.5002	-0.2024	39.663	28.697	7.864
12	3.1482	2.4359	-2.3016	10.9725	-9.4218	8.1072	-0.9052	0.4853	0.5456	-1.0075	-0.4237	-0.5667	-2.0232	1.2808	1.3288	-0.0119	-0.2346	0.2949	0.449	0.0881	0.1179	55.207	51.389	2.374
13	7.3065	1.003	-0.9489	2.6613	-1.6765	5.2493	0.6737	0.1791	0.8897	0.1562	-0.4513	-0.0642	-0.2957	0.4963	-0.2224	-0.1888	-0.1587	0.155	-0.1567	-0.1167	-0.2187	64.003	-2.226	28.808
14	6.3026	0.5958	0.7725	1.8127	0.1743	4.0606	0.7759	-1.6888	0.5165	0.6854	-0.442	-0.0964	-0.0899	0.2641	-0.334	0.1856	-0.5077	0.0832	0.3621	-0.1851	-0.2512	58.644	-6.24	49.127
15	6.4604	1.0882	-2.8494	1.6806	-0.7314	7.7792	0.7409	-0.6573	-0.1858	0.363	-0.5044	0.4802	0.4666	-0.1062	-0.2366	-0.1309	-0.3088	0.0893	-0.1169	-0.123	-0.3216	48.144	-10.683	39.483
16	13.2404	4.3404	-4.7152	8.3411	-4.9854	8.5648	0.058	-1.7739	-0.08	0.1794	0.0177	-0.5589	0.7543	0.2895	-0.0757	0.3066	-0.3303	-0.2115	0.4825	-0.3281	-0.4002	68.456	-8.994	58.436

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	938 - 962
2	X-RAY DIFFRACTION	1	A	981 - 1005
3	X-RAY DIFFRACTION	1	A	1016 - 1055
4	X-RAY DIFFRACTION	2	A	1096 - 1223
5	X-RAY DIFFRACTION	3	A	963 - 980
6	X-RAY DIFFRACTION	3	A	1006 - 1015
7	X-RAY DIFFRACTION	3	A	1080 - 1095
8	X-RAY DIFFRACTION	4	A	1056 - 1079
9	X-RAY DIFFRACTION	5	B	939 - 962
10	X-RAY DIFFRACTION	5	B	981 - 1005
11	X-RAY DIFFRACTION	5	B	1016 - 1055
12	X-RAY DIFFRACTION	6	B	1096 - 1223
13	X-RAY DIFFRACTION	7	B	963 - 980
14	X-RAY DIFFRACTION	7	B	1006 - 1015
15	X-RAY DIFFRACTION	7	B	1080 - 1095
16	X-RAY DIFFRACTION	8	B	1056 - 1079
17	X-RAY DIFFRACTION	9	C	937 - 962
18	X-RAY DIFFRACTION	9	C	981 - 1005
19	X-RAY DIFFRACTION	9	C	1016 - 1055
20	X-RAY DIFFRACTION	10	C	1096 - 1223
21	X-RAY DIFFRACTION	11	C	963 - 980
22	X-RAY DIFFRACTION	11	C	1006 - 1015
23	X-RAY DIFFRACTION	11	C	1080 - 1095
24	X-RAY DIFFRACTION	12	C	1056 - 1079
25	X-RAY DIFFRACTION	13	D	939 - 962
26	X-RAY DIFFRACTION	13	D	981 - 1005
27	X-RAY DIFFRACTION	13	D	1016 - 1055
28	X-RAY DIFFRACTION	14	D	1096 - 1223
29	X-RAY DIFFRACTION	15	D	963 - 980
30	X-RAY DIFFRACTION	15	D	1006 - 1015
31	X-RAY DIFFRACTION	15	D	1080 - 1095
32	X-RAY DIFFRACTION	16	D	1056 - 1079

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Yorodumi