PDB-4rsh: Structure of a putative lipolytic protein of G-D-S-L family from ...

ID or keywords:

Entry

Database: PDB / ID: 4rsh

Title

Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2

Components

Lipolytic protein G-D-S-L family

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

phosphatidylcholine lysophospholipase activity / membrane
Similarity search - Function

Biological species

Desulfitobacterium hafniense DCB-2 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.19 Å

Authors

Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F.

History

Deposition	Nov 7, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	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 / _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	4rsh.cif.gz	220.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4rsh.ent.gz	180.1 KB	Display	PDB format
PDBx/mmJSON format	4rsh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4rsh_validation.pdf.gz	438.1 KB	Display	wwPDB validaton report
Full document	4rsh_full_validation.pdf.gz	442 KB	Display
Data in XML	4rsh_validation.xml.gz	27 KB	Display
Data in CIF	4rsh_validation.cif.gz	37 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rs/4rsh ftp://data.pdbj.org/pub/pdb/validation_reports/rs/4rsh	HTTPS FTP

-
Related structure data

Similar structure data	6jkj-1 6vxs-2 7kxb-d 4h9j-d 7bf6-3 3ayd-d 5vpy-2 5us4-2 5zby-d 5jp5-4 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
Other databases	TargetTrack: MCSG-apc113059

Similar structure data

Other databases

TargetTrack: MCSG-apc113059

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lipolytic protein G-D-S-L family

B: Lipolytic protein G-D-S-L family

C: Lipolytic protein G-D-S-L family

hetero molecules

60.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lipolytic protein G-D-S-L family

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

2

B: Lipolytic protein G-D-S-L family

hetero molecules

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

3

C: Lipolytic protein G-D-S-L family

hetero molecules

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

Unit cell

Length a, b, c (Å)	102.997, 63.649, 85.647
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.504213, 0.054524, -0.861856), (0.00392, 0.998139, 0.060853), (0.86357, 0.027304, -0.503488)	96.9292, 18.85637, 30.68051
3	given	(-0.519365, -0.037022, -0.85375), (-0.024703, -0.997993, 0.058305), (-0.854195, 0.051372, 0.517408)	123.52134, 10.50371, 99.55444

#1: Protein	Lipolytic protein G-D-S-L family Mass: 19994.062 Da / Num. of mol.: 3 / Fragment: residues 53-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria) Strain: DCB-2 / Gene: ACL22416, Dhaf_4411 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) magic / References: UniProt: B8FVL4
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.34 Å³/Da / Density % sol: 47.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Potassium Thiocyanate, 30% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2014 / Details: beryllium lenses
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.19→85.65 Å / Num. all: 29332 / Num. obs: 29332 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / R_merge(I) obs: 0.199 / Net I/σ(I): 13.6
Reflection shell	Resolution: 2.19→2.4 Å / Redundancy: 11.1 % / R_merge(I) obs: 0.84 / Mean I/σ(I) obs: 3 / % possible all: 95.6

-
Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.8.0069	refinement
HKL-2000		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.19→30 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.86 / SU B: 15.54 / SU ML: 0.198 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26994	1480	5.1 %	RANDOM
R_work	0.19914	-	-	-
obs	0.20269	27798	98.72 %	-
all	-	27798	-	-

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: 23.771 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.91 Å²	-0 Å²	0 Å²
2-	-	0.66 Å²	-0 Å²
3-	-	-	0.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.19→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4116	0	2	311	4429

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	4200
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4029
X-RAY DIFFRACTION	r_angle_refined_deg	1.814	1.974	5697
X-RAY DIFFRACTION	r_angle_other_deg	0.86	3	9300
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.841	5	522
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.065	25.714	189
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.182	15	702
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	4.921	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	642
X-RAY DIFFRACTION	r_gen_planes_refined	0.024	0.021	4755
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	909
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	0.902	1.17	2097
X-RAY DIFFRACTION	r_mcbond_other	0.902	1.17	2096
X-RAY DIFFRACTION	r_mcangle_it	1.363	1.754	2616
X-RAY DIFFRACTION	r_mcangle_other	1.362	1.754	2617
X-RAY DIFFRACTION	r_scbond_it	1.39	1.313	2103
X-RAY DIFFRACTION	r_scbond_other	1.39	1.312	2104
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.163	1.912	3082
X-RAY DIFFRACTION	r_long_range_B_refined	4.708	5.768	5349
X-RAY DIFFRACTION	r_long_range_B_other	4.586	5.632	5249
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.19→2.247 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.326	80	-
R_work	0.303	1792	-
obs	-	-	86.67 %

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	2.1386	0.2618	2.7388	0.5567	1.2623	6.3945	0.062	-0.127	-0.1149	0.1477	-0.0957	-0.0112	0.2209	-0.1865	0.0337	0.0606	-0.0369	-0.0085	0.0308	0.0213	0.0384	42.8897	18.6595	62.6054
2	0.342	0.7217	1.2293	1.7743	2.5106	4.4615	0.1122	0.1161	-0.076	0.214	0.1365	-0.2527	0.4591	0.4558	-0.2487	0.115	0.0612	-0.0311	0.0843	0.0077	0.1005	49.1584	13.9436	54.0818
3	2.6441	3.0436	0.9799	4.5309	1.5237	1.5705	-0.0275	0.1152	-0.2044	-0.1262	0.1518	-0.3779	-0.0503	0.4045	-0.1243	0.0514	0.003	-0.0209	0.1257	-0.0156	0.0664	53.3445	21.7593	49.3397
4	7.8829	1.4465	2.2875	2.0875	0.8239	3.2644	-0.1797	0.3347	0.6709	-0.5657	0.0179	0.0477	-0.0593	0.2627	0.1618	0.1758	-0.0117	-0.0054	0.0821	0.0546	0.0722	48.4671	26.1752	43.4033
5	2.6158	1.7639	1.2806	2.9499	2.0506	2.6463	-0.0187	0.0613	0.4647	0.049	-0.1565	0.2658	-0.3511	-0.1333	0.1752	0.1931	0.0274	-0.0298	0.0368	0.0026	0.1006	44.7315	32.532	62.2896
6	1.1445	-0.0851	0.4734	2.8081	-0.2963	2.4431	0.0309	0.02	0.0062	-0.3829	-0.0585	-0.0981	0.1215	0.0953	0.0276	0.1568	0.0301	0.0356	0.0096	0.0154	0.0571	51.5012	-4.4896	29.4335
7	1.1376	-0.2914	0.2968	3.4516	-2.364	3.3229	-0.0787	0.034	0.0168	-0.2738	0.0517	0.0623	-0.1079	-0.1681	0.027	0.1195	0.0189	-0.0307	0.0133	-0.0048	0.008	39.7818	-0.4931	29.3435
8	2.7847	2.2569	-3.78	3.2803	-1.1922	7.5714	-0.0582	0.2272	0.1735	-0.4451	0.1151	0.2435	-0.399	-0.4689	-0.0569	0.1936	0.0296	-0.0534	0.1436	-0.0359	0.1121	35.3227	7.8447	30.3545
9	2.3362	1.4035	-0.5433	3.724	-1.3813	1.8599	-0.016	-0.0433	0.311	0.153	-0.1147	0.0405	-0.4318	-0.0119	0.1306	0.2413	0.0254	-0.0601	0.0116	-0.019	0.0941	45.2287	11.0411	34.0226
10	3.2571	-1.215	-0.5682	1.6722	-1.4797	4.0398	0.0495	-0.1261	0.2359	-0.1641	0.0348	-0.164	-0.2922	0.2593	-0.0843	0.2569	-0.0541	0.0129	0.0374	-0.0274	0.1626	56.0585	9.3962	29.607
11	2.777	-1.565	0.2836	1.1557	-0.6419	2.2634	0.1312	-0.1325	-0.0508	0.0998	-0.0363	0.1238	-0.3148	-0.2267	-0.0949	0.2035	-0.0476	0.0492	0.1633	-0.0473	0.1522	72.9896	-8.118	50.2268
12	1.2939	1.0206	0.5075	2.6102	-0.5255	3.2435	0.0949	0.032	0.117	-0.2169	-0.114	0.1049	-0.1653	-0.1119	0.019	0.1095	0.043	0.0249	0.0376	-0.0171	0.0491	77.4437	-5.0821	38.7638
13	2.1563	1.7966	0.135	2.9071	-0.1716	1.8179	0.0535	0.0351	-0.0206	-0.3141	-0.1461	-0.0365	0.1373	-0.0259	0.0926	0.102	0.0395	0.0191	0.0267	-0.0055	0.0441	80.5504	-15.4263	36.7417
14	4.9059	2.0334	-0.4202	3.3272	-1.3277	1.1766	-0.1187	0.0175	-0.1837	-0.2334	-0.0954	-0.0197	0.1963	-0.0192	0.2141	0.1195	-0.0263	0.0298	0.0211	-0.0258	0.0913	75.6999	-21.4432	45.2145
15	2.1212	-1.0049	0.1452	2.8005	-0.9976	3.5946	-0.1	-0.2834	-0.0604	0.0413	-0.0673	0.1475	0.002	-0.0741	0.1673	0.0609	-0.0144	0.0334	0.0749	-0.0255	0.0517	73.557	-17.5744	51.8241

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	53 - 94
2	X-RAY DIFFRACTION	2	A	95 - 125
3	X-RAY DIFFRACTION	3	A	126 - 168
4	X-RAY DIFFRACTION	4	A	169 - 185
5	X-RAY DIFFRACTION	5	A	186 - 227
6	X-RAY DIFFRACTION	6	B	53 - 111
7	X-RAY DIFFRACTION	7	B	112 - 166
8	X-RAY DIFFRACTION	8	B	167 - 178
9	X-RAY DIFFRACTION	9	B	179 - 201
10	X-RAY DIFFRACTION	10	B	202 - 227
11	X-RAY DIFFRACTION	11	C	53 - 82
12	X-RAY DIFFRACTION	12	C	83 - 146
13	X-RAY DIFFRACTION	13	C	147 - 179
14	X-RAY DIFFRACTION	14	C	180 - 207
15	X-RAY DIFFRACTION	15	C	208 - 227

-
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