PDB-2q78: Crystal structure of a thioesterase-like protein (tm0581) from th...

ID or keywords:

Entry

Database: PDB / ID: 2q78

Title

Crystal structure of a thioesterase-like protein (tm0581) from thermotoga maritima msb8 at 2.20 A resolution

Components

Uncharacterized protein

Keywords

HYDROLASE /

Structural genomics / Joint Center for Structural Genomics / JCSG /

Protein Structure Initiative / PSI-2

Function / homology

Fluoroacetyl-CoA thioesterase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / MALONYL-COENZYME A / Uncharacterized protein

Function and homology information

Biological species

Thermotoga maritima MSB8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of Uncharacterized protein TM0581 (TM0581) from Thermotoga maritima at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jun 6, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Oct 25, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 ...

Remark 999

SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2q78.cif.gz	236.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2q78.ent.gz	196 KB	Display	PDB format
PDBx/mmJSON format	2q78.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/q7/2q78 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/2q78	HTTPS FTP

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Related structure data

Similar structure data	2ydy-d 1sw1-2 5oei-d 4bb4-d 3r6u-d 4chg-3 4chg-2 5tcy-3 3f6x-3 5lq1-1 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 - HomologyF&H Search
Other databases	TargetDB: 282454

Similar structure data

Other databases

TargetDB: 282454

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

C: Uncharacterized protein

D: Uncharacterized protein

E: Uncharacterized protein

F: Uncharacterized protein

G: Uncharacterized protein

H: Uncharacterized protein

hetero molecules

148 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

defined by author&software
Evidence: gel filtration
37 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Uncharacterized protein

D: Uncharacterized protein

hetero molecules

defined by author&software
Evidence: gel filtration
37 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Uncharacterized protein

F: Uncharacterized protein

hetero molecules

defined by author&software
Evidence: gel filtration
37 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Uncharacterized protein

H: Uncharacterized protein

hetero molecules

defined by author&software
Evidence: gel filtration
37 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	60.347, 90.706, 230.420
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 3 - 130 / Label seq-ID: 15 - 142

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H

Details

SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

#1: Protein	Uncharacterized protein Mass: 17633.559 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: TM_0581 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9WZ50
#2: Chemical	ChemComp-MLC / MALONYL-COENZYME A / Malonyl-CoA Mass: 853.580 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₄H₃₈N₇O₁₉P₃S
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.23 Å³/Da / Density % sol: 44.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NANODROP, 0.8M Lithium chloride, 10.0% PEG 6000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97913 Å

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2007 / Details: Flat collimating mirror, toroid focusing mirror

Radiation

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

Radiation wavelength

Wavelength: 0.97913 Å / Relative weight: 1

Reflection

Resolution: 2.2→29.975 Å / Num. obs: 65127 / % possible obs: 99.7 % / Redundancy: 4.8 % / B_iso Wilson estimate: 37.8 Å² / R_merge(I) obs: 0.112 / R_sym value: 0.112 / Net I/σ(I): 10.4

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
2.2-2.26	3.9	0.752	1.6	17882	4604	0.752	96.8
2.26-2.32	4.8	0.692	1.1	22420	4646	0.692	100
2.32-2.39	5	0.619	1.2	22363	4502	0.619	100
2.39-2.46	5	0.571	1.3	21788	4383	0.571	100
2.46-2.54	5	0.469	1.6	21160	4243	0.469	100
2.54-2.63	5	0.365	2.1	20702	4149	0.365	100
2.63-2.73	5	0.289	2.6	19866	3993	0.289	100
2.73-2.84	5	0.223	3.4	19023	3828	0.223	100
2.84-2.97	5	0.18	4.2	18279	3686	0.18	100
2.97-3.11	5	0.15	5	17615	3545	0.15	100
3.11-3.28	5	0.12	6.1	16690	3365	0.12	100
3.28-3.48	5	0.089	7.9	15775	3186	0.089	100
3.48-3.72	4.9	0.079	4.6	14917	3019	0.079	100
3.72-4.02	4.9	0.073	8.6	13885	2831	0.073	100
4.02-4.4	4.9	0.067	9.2	12592	2593	0.067	100
4.4-4.92	4.8	0.061	10.4	11423	2366	0.061	100
4.92-5.68	4.8	0.069	9.2	10109	2120	0.069	100
5.68-6.96	4.6	0.072	9.2	8374	1808	0.072	100
6.96-9.84	4.5	0.063	7.9	6440	1438	0.063	100
9.84-29.98	4.1	0.054	10	3345	822	0.054	96.6

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
SCALA		data scaling
PDB_EXTRACT	3	data extraction
MAR345	CCD	data collection
MOSFLM		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.2→29.975 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.941 / SU B: 10.66 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.193
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. RESIDUES A/B/C/D/E/G131-141 AND F134-141 AND MOST OF THE N_TERMINAL PURIFICATION TAG ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	3296	5.1 %	RANDOM
R_work	0.175	-	-	-
obs	0.177	65047	99.73 %	-

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: 43.94 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.06 Å²	0 Å²	0 Å²
2-	-	-0.45 Å²	0 Å²
3-	-	-	-0.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.975 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8219	0	434	282	8935

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	8989
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5998
X-RAY DIFFRACTION	r_angle_refined_deg	1.572	2.023	12277
X-RAY DIFFRACTION	r_angle_other_deg	0.883	3	14549
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.433	5	1104
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.571	21.721	366
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.733	15	1535
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.92	15	104
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	1466
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9713
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1907
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	1560
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	6541
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	4246
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	5139
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.15	0.2	281
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.076	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.133	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.284	0.2	72
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.151	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.855	3	5465
X-RAY DIFFRACTION	r_mcbond_other	0.585	3	2173
X-RAY DIFFRACTION	r_mcangle_it	2.761	5	8649
X-RAY DIFFRACTION	r_scbond_it	5.367	8	3944
X-RAY DIFFRACTION	r_scangle_it	7.379	11	3601

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	717	MEDIUM POSITIONAL	0.29	0.5
2	B	717	MEDIUM POSITIONAL	0.24	0.5
3	C	717	MEDIUM POSITIONAL	0.39	0.5
4	D	717	MEDIUM POSITIONAL	0.27	0.5
5	E	717	MEDIUM POSITIONAL	0.22	0.5
6	F	717	MEDIUM POSITIONAL	0.31	0.5
7	G	717	MEDIUM POSITIONAL	0.25	0.5
8	H	717	MEDIUM POSITIONAL	0.24	0.5
1	A	704	LOOSE POSITIONAL	0.51	5
2	B	704	LOOSE POSITIONAL	0.47	5
3	C	704	LOOSE POSITIONAL	0.64	5
4	D	704	LOOSE POSITIONAL	0.68	5
5	E	704	LOOSE POSITIONAL	0.45	5
6	F	704	LOOSE POSITIONAL	0.64	5
7	G	704	LOOSE POSITIONAL	0.5	5
8	H	704	LOOSE POSITIONAL	0.46	5
1	A	717	MEDIUM THERMAL	1.42	2
2	B	717	MEDIUM THERMAL	0.96	2
3	C	717	MEDIUM THERMAL	0.84	2
4	D	717	MEDIUM THERMAL	1.15	2
5	E	717	MEDIUM THERMAL	0.64	2
6	F	717	MEDIUM THERMAL	0.85	2
7	G	717	MEDIUM THERMAL	0.75	2
8	H	717	MEDIUM THERMAL	0.69	2
1	A	704	LOOSE THERMAL	3.44	10
2	B	704	LOOSE THERMAL	2.7	10
3	C	704	LOOSE THERMAL	3.25	10
4	D	704	LOOSE THERMAL	4.99	10
5	E	704	LOOSE THERMAL	2.61	10
6	F	704	LOOSE THERMAL	3.18	10
7	G	704	LOOSE THERMAL	2.19	10
8	H	704	LOOSE THERMAL	2.36	10

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.278	223	-
R_work	0.224	4350	-
obs	-	4573	96.31 %

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	0.7325	-0.2088	0.0133	0.9057	0.156	0.0351	0.1146	0.0109	0.1456	-0.0049	-0.003	-0.0177	-0.1602	0.1013	-0.1116	-0.1636	-0.001	-0.0171	-0.0756	0.0373	-0.1036	26.285	-4.401	-19.378
2	0.485	-0.1972	0.4034	1.3754	-0.8667	2.9992	-0.0301	0.2427	-0.0078	-0.2843	-0.0807	-0.0002	0.1569	0.0938	0.1108	-0.086	0.0231	0.0156	-0.0408	0.0213	-0.1157	24.565	-11.908	-36.297
3	2.2962	-0.1676	-0.5288	1.1419	-0.0611	2.6154	0.0728	0.2791	0.2455	-0.0014	0.0133	0.1974	-0.2141	-0.302	-0.0861	-0.1477	0.0503	0.0081	-0.0784	0.1139	0.0233	56.214	1.695	-12.229
4	1.2258	0.0323	-0.0239	0.5842	-0.5641	2.0275	0.0627	-0.0539	0.1286	0.1393	0.0123	0.1386	-0.1539	-0.2367	-0.075	-0.1524	-0.0035	0.0439	-0.1091	0.0383	-0.051	55.715	-8.898	2.761
5	0.9834	0.3608	-0.4877	1.8405	-1.8546	5.7846	-0.1474	-0.3101	0.3049	0.7726	-0.1925	-0.2396	-1.111	0.2977	0.3399	0.4706	-0.0788	-0.1489	-0.0108	-0.0793	0.1455	76.342	12.751	33.28
6	1.4841	0.4458	0.8461	1.9869	-0.4926	3.7037	-0.0268	-0.1588	0.0442	0.3138	-0.2052	-0.4844	-0.4402	0.5471	0.232	-0.0571	-0.087	-0.0562	-0.0168	0.0366	0.117	82.205	5.703	16.854
7	1.3422	0.332	0.1104	4.1489	0.0538	3.4307	-0.0847	0.0871	0.1232	-0.2914	-0.0984	-0.2625	-0.2001	0.344	0.1832	0.0381	-0.0209	0.0485	0.0195	0.1351	-0.0118	23.557	15.174	-66.237
8	0.8411	-0.1545	0.0113	2.3623	-1.7374	4.4355	-0.0475	-0.1281	0.1058	0.276	0.1003	0.1676	-0.6465	-0.3177	-0.0528	0.0389	0.0514	0.0221	0.0334	0.0571	-0.0358	11.412	14.283	-52.11

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-4 - 130	8 - 142
2	X-RAY DIFFRACTION	2	B	B	0 - 130	12 - 142
3	X-RAY DIFFRACTION	3	C	C	0 - 130	12 - 142
4	X-RAY DIFFRACTION	4	D	D	1 - 130	13 - 142
5	X-RAY DIFFRACTION	5	E	E	0 - 130	12 - 142
6	X-RAY DIFFRACTION	6	F	F	-2 - 133	10 - 145
7	X-RAY DIFFRACTION	7	G	G	0 - 130	12 - 142
8	X-RAY DIFFRACTION	8	H	H	0 - 130	12 - 142

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