PDB-3leq: The Crystal Structure of the Roadblock/LC7 domain from Streptomyc...

ID or keywords:

Entry

Database: PDB / ID: 3leq

Title

The Crystal Structure of the Roadblock/LC7 domain from Streptomyces avermitillis to 1.85A

Components

uncharacterized protein cvnB5

Keywords

structure genomics / unknown function / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

: / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / Roadblock/LAMTOR2 domain-containing protein

Function and homology information

Biological species

Streptomyces avermitilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.85 Å

Authors

Stein, A.J. / Xu, X. / Cui, H. / Ng, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of the Roadblock/LC7 domain from Streptomyces avermitillis to 1.85A
Authors: Stein, A.J. / Xu, X. / Cui, H. / Ng, J. / Edwards, A. / Savchenko, A. / Joachimiak, A.

History

Deposition	Jan 15, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 22, 2012	Group: Structure summary
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.4	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 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3leq.cif.gz	34.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3leq.ent.gz	23 KB	Display	PDB format
PDBx/mmJSON format	3leq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	3hoh-2 5hoh-3 2hoh-1 1f8h-d 4hoh-3 2ctn-d 4hoh-2 1i0x-1 1ff1-d 4a0e-1 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: APC65473.1

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized protein cvnB5

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

1

Idetical with deposited unit
defined by author

2

A: uncharacterized protein cvnB5

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

Unit cell

Length a, b, c (Å)	89.466, 29.824, 40.752
Angle α, β, γ (deg.)	90.00, 104.89, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	uncharacterized protein cvnB5 / Roadblock/LC7 domain Mass: 13557.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: cvnB5, SAV2189, SAV_2189 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q82L23
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THIS WAS A IN SITU PROTEOLYSIS CRYSTAL STRUCTURE

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.94 Å³/Da / Density % sol: 36.52 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 8.5 Details: 2M Ammonium phosphate, 0.1M Tris pH 8.5, vapor diffusion, temperature 289K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2009

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 1.85→50 Å / Num. obs: 8867 / % possible obs: 98.5 % / Redundancy: 3.6 % / R_merge(I) obs: 0.083 / Net I/σ(I): 16

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.85-1.92	3.7	0.561	1	99
1.92-1.99	3.6	0.394	1	98.6
1.99-2.08	3.6	0.249	1	99.9
2.08-2.19	3.6	0.172	1	98.9
2.19-2.33	3.6	0.123	1	99.4
2.33-2.51	3.6	0.113	1	99.6
2.51-2.76	3.6	0.102	1	99.7
2.76-3.16	3.6	0.082	1	99.9
3.16-3.99	3.4	0.062	1	99.4
3.99-50	3.3	0.063	1	91.5

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0102	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 1.85→43.23 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.941 / SU B: 7.664 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. this was a in situ proteolysis crystal structure so there is higher than usual degree of disorder.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23588	416	4.7 %	RANDOM
R_work	0.21592	-	-	-
obs	0.21693	8446	98.16 %	-

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: 10.915 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	0 Å²	-1.44 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	-0.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→43.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	722	0	0	37	759

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	744
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.238	1.993	1015
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.703	5	106
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.571	23.636	22
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.141	15	123
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.198	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	135
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	525
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	0.526	1.5	508
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.901	2	803
X-RAY DIFFRACTION	r_scbond_it	1.884	3	236
X-RAY DIFFRACTION	r_scangle_it	2.646	4.5	209
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.854→1.902 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	26	-
R_work	0.235	574	-
obs	-	-	93.6 %

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	23.4351	1.9727	-1.4875	19.3842	-12.423	30.5076	0.6009	1.1023	0.5116	-0.4387	-0.2142	0.3842	-0.1854	-1.1861	-0.3867	0.2145	0.0339	-0.0152	0.2976	-0.0385	0.1886	29.9031	21.6866	-5.6108
2	10.882	4.8145	3.0628	14.9256	-4.7345	7.7622	-0.2188	0.022	-0.2572	-0.4798	0.1343	-0.3201	0.4681	-0.5882	0.0845	0.1644	-0.0269	-0.0526	0.14	-0.0451	0.2016	29.4771	17.6544	0.8864
3	9.2301	0.2525	-4.5263	12.0695	-1.4926	7.6471	0.2578	-0.0122	-0.2511	0.0484	-0.4276	0.8868	0.5443	-0.8455	0.1698	0.1332	-0.1161	-0.034	0.3344	-0.0399	0.2377	25.2301	15.6897	7.6268
4	15.8973	2.9391	-2.7978	13.2981	0.3594	11.0691	0.1193	0.1039	0.7056	-0.3696	-0.0075	-0.6633	-0.6704	0.2796	-0.1117	0.1984	0.0127	0.0125	0.0872	0.0077	0.1527	37.6038	27.518	4.3064
5	28.9483	13.7521	2.4244	14.4734	1.029	7.6029	-0.335	1.1251	0.8251	-1.0515	0.3918	0.178	-0.5212	-0.2396	-0.0568	0.2631	0.0444	-0.0311	0.1236	0.0116	0.1484	33.3967	28.5436	1.2575
6	2.6357	-4.1656	-2.51	20.8685	0.684	10.3871	-0.4008	0.7079	0.2844	-0.3504	-0.2383	1.0839	-2.2983	-3.1866	0.6391	0.5975	0.4037	-0.5663	0.6701	-0.175	0.777	25.3335	29.9475	4.4777
7	21.9773	1.6987	15.0221	9.3884	-1.7333	20.3295	-0.0625	0.0526	0.6436	0.1823	0.187	0.4425	-1.2352	0.2291	-0.1245	0.2339	0.0208	0.0045	0.0516	-0.0032	0.1786	33.6033	32.1137	11.4692
8	3.7226	-12.1933	-2.9836	14.7932	2.2353	-4.4164	0.3914	0.5533	0.1372	-0.6755	-0.8572	-0.806	-0.0952	0.2741	0.4659	0.3231	-0.2022	0.0785	0.641	0.0767	0.6769	43.6664	28.4646	15.279
9	86.0892	8.3119	-46.562	8.0237	-5.2248	49.5746	-0.1629	-1.5799	0.3807	0.1314	-0.391	0.4746	0.5898	0.0418	0.5539	0.1347	-0.061	-0.0323	0.3758	-0.0249	0.0834	35.9939	20.5714	19.1076
10	32.3491	7.2315	-14.1934	13.1238	-4.1657	24.518	0.3658	-1.2588	0.5623	0.9878	-0.417	1.0522	0.5428	-0.8994	0.0511	0.1322	-0.0615	0.0583	0.2392	-0.0565	0.1571	30.8203	20.4085	17.9418
11	8.9213	2.2523	-13.2286	1.9515	-5.3044	18.4146	-0.1109	-0.7537	0.2899	-0.4082	0.0352	-0.2457	0.3883	0.909	0.0757	0.149	-0.052	0.0865	0.2104	-0.0027	0.2433	43.14	21.847	5.7247
12	19.598	2.1806	-12.1117	6.1563	-0.4541	16.4645	-0.065	-0.5255	-0.0452	-0.0823	-0.1289	0.2077	0.0382	0.0628	0.1939	0.058	0.0113	-0.009	0.0805	-0.013	0.0976	33.0836	21.2877	10.379
13	14.6222	-18.3279	-22.449	28.1098	18.0638	33.7681	-1.1548	-0.8267	-0.6849	1.5878	0.8765	1.1752	1.1936	0.1771	0.2783	0.3428	-0.0471	0.0904	0.504	0.1188	0.2366	29.7887	11.6376	16.8274
14	3.5483	-5.0071	-4.3555	14.1178	1.0572	17.1182	-0.0575	-0.1639	0.2365	0.1824	0.1558	-0.1469	0.0869	-0.0232	-0.0983	0.1375	-0.0106	0.0249	0.1018	-0.0007	0.1619	35.2142	11.1669	8.7041
15	19.8002	9.5151	-5.8822	24.9808	-1.3152	33.527	-0.2627	0.1413	-0.0813	-1.8095	0.0644	-1.2253	0.0592	0.5464	0.1983	0.2249	-0.0002	0.1027	0.1202	-0.0422	0.2238	38.2828	13.31	1.1439

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 14
2	X-RAY DIFFRACTION	2	A	15 - 19
3	X-RAY DIFFRACTION	3	A	20 - 28
4	X-RAY DIFFRACTION	4	A	29 - 35
5	X-RAY DIFFRACTION	5	A	36 - 42
6	X-RAY DIFFRACTION	6	A	43 - 50
7	X-RAY DIFFRACTION	7	A	51 - 59
8	X-RAY DIFFRACTION	8	A	60 - 77
9	X-RAY DIFFRACTION	9	A	78 - 83
10	X-RAY DIFFRACTION	10	A	84 - 89
11	X-RAY DIFFRACTION	11	A	90 - 97
12	X-RAY DIFFRACTION	12	A	98 - 104
13	X-RAY DIFFRACTION	13	A	105 - 111
14	X-RAY DIFFRACTION	14	A	112 - 117
15	X-RAY DIFFRACTION	15	A	118 - 123

-
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