PDB-3rqb: Crystal Structure of Conserved Protein of Unknown Function with H...

ID or keywords:

Entry

Database: PDB / ID: 3rqb

Title

Crystal Structure of Conserved Protein of Unknown Function with Hot dog Fold from Alicyclobacillus acidocaldarius

Components

Uncharacterized protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta sandwich / hotdog fold

Function / homology

Function and homology information

: / : / Acyl-CoA thioesterase C-terminal domain / Acyl-CoA thioesterase, double hotdog domain / Acyl-CoA thioesterase, double hotdog domain / : / Acyl-CoA thioesterase N-terminal domain / Porin / HotDog domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology

Biological species

Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Kim, Y. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of Conserved Protein of Unknown Function with Hot_dog Fold from Alicyclobacillus acidocaldarius
Authors: Kim, Y. / Chhor, G. / Bearden, J. / Joachimiak, A.

History

Deposition	Apr 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 18, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 30, 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 / _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

-
Download

PDBx/mmCIF format	3rqb.cif.gz	219.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3rqb.ent.gz	180 KB	Display	PDB format
PDBx/mmJSON format	3rqb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3rqb_validation.pdf.gz	444.9 KB	Display	wwPDB validaton report
Full document	3rqb_full_validation.pdf.gz	456.7 KB	Display
Data in XML	3rqb_validation.xml.gz	24.3 KB	Display
Data in CIF	3rqb_validation.cif.gz	31.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rq/3rqb ftp://data.pdbj.org/pub/pdb/validation_reports/rq/3rqb	HTTPS FTP

-
Related structure data

Similar structure data	5m8l-4 3sq7-1 5m8p-4 4dwr-3 6bk1-d 5m8n-4 4pex-2 5m8r-3 5m8m-2 4tz5-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC100327

-
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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	109.645, 109.645, 192.614
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	B-284- HOH

#1: Protein	Uncharacterized protein Mass: 30759.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria) Strain: DSM 446 / Gene: Aaci_2638 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: C8WTQ0
#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.: 51 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.72 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2 M Calcium Acetate, 0.1 M Sodium Acetate:Acetic Acid pH 4.5 30% (v/v) PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.8→47.48 Å / Num. all: 17458 / Num. obs: 17458 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / B_iso Wilson estimate: 53.55 Å² / R_sym value: 0.15 / Net I/σ(I): 6.4
Reflection shell	Resolution: 2.8→2.85 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 832 / R_sym value: 0.877 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
PHENIX		model building
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.8→47.478 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.65 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.257	1777	10.55 %	random
R_work	0.175	-	-	-
all	0.179	16840	-	-
obs	0.179	16840	95.92 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 27.933 Å² / k_sol: 0.315 e/Å³

Displacement parameters

B_iso mean: 58 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.6992 Å²	-0 Å²	0 Å²
2-	-	-8.6992 Å²	-0 Å²
3-	-	-	17.3984 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→47.478 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4132	0	3	51	4186

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4267
X-RAY DIFFRACTION	f_angle_d	1.243	5844
X-RAY DIFFRACTION	f_dihedral_angle_d	15.757	1516
X-RAY DIFFRACTION	f_chiral_restr	0.074	653
X-RAY DIFFRACTION	f_plane_restr	0.006	761

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
2.8011-2.8835	0.3176	127	0.2576	1135	1262	80
2.8835-2.9765	0.3314	131	0.252	1185	1316	84
2.9765-3.0829	0.3311	133	0.2469	1198	1331	85
3.0829-3.2063	0.3748	136	0.2337	1225	1361	86
3.2063-3.3521	0.3055	137	0.2125	1231	1368	86
3.3521-3.5288	0.2967	140	0.199	1262	1402	88
3.5288-3.7498	0.2542	139	0.1687	1244	1383	87
3.7498-4.0391	0.2698	142	0.1559	1282	1424	88
4.0391-4.4452	0.2328	143	0.1456	1291	1434	88
4.4452-5.0875	0.1811	146	0.1264	1310	1456	89
5.0875-6.4062	0.2581	149	0.153	1338	1587	89
6.4062-42.5891	0.2231	161	0.1418	1449	1610	89

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	2.149	1.0244	1.3082	3.722	1.8656	2.391	0.2493	-0.33	-0.0483	0.5522	0.0268	-0.1174	0.3421	-0.1386	-0.1537	0.4776	-0.0122	-0.0168	0.5496	-0.0394	0.6049	55.9033	56.2636	99.3283
2	0.441	0.485	0.2092	0.9428	0.8408	1.0683	0.0063	-0.0082	0.1521	0.1012	-0.0892	0.1288	-0.0435	0.3514	0.0435	0.4738	0.0835	-0.0163	0.4447	0.0293	0.5771	59.2682	48.5489	89.5673
3	0.9392	-0.3403	-0.4178	0.9359	-0.0328	0.6782	0.2299	-0.2559	0.0523	-0.062	0.0299	-0.0152	0.0944	0.0606	-0.0987	0.2871	0.0327	0.0037	0.3214	0.0358	0.297	51.8907	63.1381	90.4382
4	0.9449	-0.1043	-0.4813	0.9214	0.7625	1.3922	0.0702	-0.2074	-0.0696	-0.0867	0.2771	-0.1932	-0.2494	0.244	-0.2081	0.413	0.0042	0.0163	0.3828	0.0282	0.3382	58.8076	65.2273	90.1711
5	0.7609	0.5689	-0.0504	1.1141	-0.1015	0.888	0.15	-0.1264	-0.3214	0.2332	-0.1795	-0.2715	-0.052	-0.0171	0.0596	0.3344	-0.0469	-0.0409	0.3432	0.0412	0.3591	59.0647	64.7355	87.5302
6	0.1717	0.0993	0.0035	0.8952	-0.1028	0.307	-0.0792	-0.127	-0.0066	-0.0797	0.2234	0.3976	-0.0533	-0.2031	-0.0121	0.38	-0.0192	0.0105	0.3795	-0.0263	0.4475	30.4378	59.1994	80.6591
7	1.7544	-0.228	-0.1012	0.6605	0.5198	0.8501	-0.353	-0.0735	-0.7173	0.051	0.1947	0.1949	0.5268	-0.0283	-0.1097	0.4637	0.0361	0.0228	0.3842	-0.0999	0.6745	44.802	39.8223	83.5632
8	0.4343	-0.0337	0.0598	0.6973	0.6855	1.0399	-0.2219	0.0369	-0.631	-0.114	0.1015	0.5039	-0.0601	0.0259	0.117	0.4687	-0.0463	0.1372	0.3622	-0.0451	0.673	40.8579	44.9352	79.9864
9	0.9034	0.3896	-0.1284	0.3928	-0.4484	0.7756	0.0058	-0.0722	-0.4208	-0.1192	-0.0935	-0.2148	-0.0526	-0.0629	0.0489	0.3004	-0.0451	0.0093	0.23	-0.0147	0.3801	45.1637	52.6161	78.6172
10	0.2235	-0.1297	0.0185	0.4353	0.1162	0.0276	0.1271	0.0917	0.3071	0.0611	-0.1601	-0.0808	-0.0702	-0.0779	-0.0074	0.4599	0.008	-0.0076	0.3649	0.0037	0.5919	40.256	54.479	76.8038
11	0.6382	-0.761	-0.37	1.1895	0.6349	0.359	0.2417	0.0875	0.451	-0.5641	0.125	-0.4614	0.0009	-0.0264	-0.2057	0.4712	-0.012	0.0122	0.2593	0.0246	0.5002	51.7444	53.0489	71.7961
12	1.5042	-0.2833	0.6118	0.9192	0.4501	0.6626	0.1726	0.0505	0.2427	0.1355	-0.0119	-0.6162	0.0569	0.0451	-0.032	0.3633	-0.0193	0.0012	0.4128	0.063	0.5332	64.5305	82.7842	67.5553
13	3.9198	-0.3482	-1.2547	1.0455	-0.0586	0.3901	0.4282	0.3224	0.552	-0.108	-0.1961	0.0369	0.1576	-0.1511	-0.0322	0.5011	-0.0409	0.0182	0.4756	0.0221	0.3828	53.3731	80.6232	69.9687
14	0.631	-0.0614	-0.0635	0.2117	0.1114	0.2332	-0.057	-0.2003	-0.0843	-0.1235	0.0448	-0.0321	0.2064	0.0284	0.0812	0.3705	0.0193	0.0985	0.3372	-0.0521	0.3445	62.591	68.5075	71.3312
15	1.1465	-0.2167	-0.1366	1.3362	-0.3203	0.2294	-0.1522	-0.2648	-0.1496	0.2113	0.1761	-0.2633	-0.004	-0.0329	0.0489	0.2301	-0.034	0.0153	0.2372	0.0592	0.2728	62.9915	73.8	77.2035
16	0.6655	-0.4676	0.4047	0.3677	0.0305	0.6551	0.047	0.2427	-0.0757	0.08	0.0257	0.0929	-0.0504	0.1799	-0.0183	0.2747	-0.038	0.0446	0.2984	-0.0185	0.2624	54.9981	65.5158	68.2701
17	0.4521	-0.2407	0.206	0.1592	-0.0217	0.2891	-0.0759	0.1395	-0.1306	-0.0959	0.0248	0.0441	-0.0951	-0.0104	-0.0042	0.3708	-0.0038	0.0295	0.396	0.0133	0.2707	40.438	76.7268	58.6987
18	0.7971	-0.1178	0.1312	0.6425	-0.1771	0.048	0.1131	0.2251	-0.1624	-0.1256	-0.0152	0.0503	-0.265	0.0551	0.1483	0.2492	0.0119	0.029	0.253	-0.0176	0.1548	44.2868	68.9439	65.9948
19	0.9367	-0.7972	-1.4763	1.2333	0.6734	3.4978	-0.3095	-0.075	0.0857	0.2	-0.2909	0.1766	0.2387	0.2435	-0.0318	0.3647	0.0256	-0.0384	0.3575	-0.1084	0.4183	40.2676	70.6653	74.7992

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 5:21)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 22:37)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 38:66)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 67:87)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 88:110)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 111:131)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 132:153)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 154:178)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 179:239)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 240:253)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 254:268)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 4:25)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 26:50)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 51:66)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 67:87)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 88:130)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 131:178)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 179:253)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 254:268)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi