PDB-6vbf: 1.85 Angstrom Resolution Crystal Structure of N-terminal Domain o...

ID or keywords:

Entry

Database: PDB / ID: 6vbf

Title

1.85 Angstrom Resolution Crystal Structure of N-terminal Domain of Two-component System Response Regulator from Acinetobacter baumannii

Components

Two-component regulatory system response regulator

Keywords

TRANSCRIPTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / two-component system response regulator

Function / homology

Function and homology information

phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.85 Angstrom Resolution Crystal Structure of N-terminal Domain of Two-component System Response Regulator from Acinetobacter baumannii
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 18, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6vbf.cif.gz	111.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6vbf.ent.gz	84.2 KB	Display	PDB format
PDBx/mmJSON format	6vbf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6vbf_validation.pdf.gz	423.7 KB	Display	wwPDB validaton report
Full document	6vbf_full_validation.pdf.gz	424.2 KB	Display
Data in XML	6vbf_validation.xml.gz	14.2 KB	Display
Data in CIF	6vbf_validation.cif.gz	18.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vb/6vbf ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vbf	HTTPS FTP

-
Related structure data

Similar structure data	4hhg-2 5hm6-2 2h1g-d 6ont-1 2h1d-d 1su9-d 3c73-d 3gru-d 3ewl-d 2h1a-d 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: CSGID-IDP95894

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (10) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Two-component regulatory system response regulator

B: Two-component regulatory system response regulator

hetero molecules

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

1

B: Two-component regulatory system response regulator

hetero molecules

A: Two-component regulatory system response regulator

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.819, 51.819, 194.504
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Two-component regulatory system response regulator Mass: 14501.115 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: rstA, NCTC13305_01717 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): magic / References: UniProt: A0A380UY17
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.1 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 7.6 mg/ml, 0.01M Tris pH 8.3; Screen: PEGs II (H8), 0.2M Calcium acetate, 0.1M HEPES pH 7.5, 10% (w/v) PEG 8000. Cryo: 0.2M Calcium chloride, 0.1M HEPES pH 7.5, 30 %(w/v) PEG 4000.

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2019 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.85→30 Å / Num. obs: 25198 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / B_iso Wilson estimate: 29.2 Å² / R_merge(I) obs: 0.071 / R_pim(I) all: 0.029 / R_rim(I) all: 0.077 / R_sym value: 0.071 / Χ²: 1.268 / Net I/σ(I): 28.2
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.776 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1210 / CC_1/2: 0.905 / CC star: 0.975 / R_pim(I) all: 0.318 / R_rim(I) all: 0.839 / R_sym value: 0.776 / Χ²: 1.001 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.85→29.394 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.947 / SU B: 6.047 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2161	1255	5.006 %
R_work	0.1778	-	-
all	0.18	-	-
obs	-	25072	99.952 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 35.519 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.662 Å²	0.331 Å²	0 Å²
2-	-	0.662 Å²	0 Å²
3-	-	-	-2.146 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→29.394 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1908	0	5	141	2054

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	2025
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	2004
X-RAY DIFFRACTION	r_angle_refined_deg	1.424	1.661	2727
X-RAY DIFFRACTION	r_angle_other_deg	0.38	1.579	4619
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.546	5	254
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.862	19.839	124
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.719	15	356
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.526	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	262
X-RAY DIFFRACTION	r_gen_planes_refined	0.053	0.02	2263
X-RAY DIFFRACTION	r_gen_planes_other	0.049	0.02	416
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	393
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	1835
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	946
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	926
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	137
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.121	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.214	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.286	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.027	2.233	1014
X-RAY DIFFRACTION	r_mcbond_other	1.926	2.207	1003
X-RAY DIFFRACTION	r_mcangle_it	2.758	3.289	1258
X-RAY DIFFRACTION	r_mcangle_other	2.758	3.291	1259
X-RAY DIFFRACTION	r_scbond_it	2.458	2.573	1011
X-RAY DIFFRACTION	r_scbond_other	2.457	2.574	1012
X-RAY DIFFRACTION	r_scangle_it	3.56	3.724	1469
X-RAY DIFFRACTION	r_scangle_other	3.559	3.726	1470
X-RAY DIFFRACTION	r_lrange_it	5.76	27.444	2183
X-RAY DIFFRACTION	r_lrange_other	5.666	26.901	2150

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.85-1.898	0.289	89	0.263	1726	0.264	1816	0.796	0.836	99.9449	0.234
1.898-1.95	0.268	93	0.226	1708	0.228	1802	0.844	0.883	99.9445	0.198
1.95-2.006	0.202	96	0.21	1655	0.21	1751	0.928	0.916	100	0.188
2.006-2.067	0.22	88	0.183	1621	0.185	1709	0.927	0.938	100	0.164
2.067-2.135	0.257	59	0.186	1582	0.188	1641	0.901	0.934	100	0.168
2.135-2.209	0.25	94	0.178	1495	0.182	1589	0.923	0.941	100	0.165
2.209-2.292	0.182	64	0.172	1479	0.173	1543	0.949	0.952	100	0.161
2.292-2.385	0.21	68	0.156	1418	0.158	1486	0.944	0.96	100	0.146
2.385-2.491	0.164	69	0.163	1371	0.163	1440	0.959	0.956	100	0.156
2.491-2.611	0.201	73	0.16	1273	0.162	1346	0.95	0.953	100	0.159
2.611-2.751	0.236	72	0.191	1231	0.194	1303	0.927	0.939	100	0.19
2.751-2.916	0.221	52	0.172	1174	0.174	1226	0.943	0.953	100	0.177
2.916-3.116	0.222	54	0.185	1093	0.187	1147	0.922	0.943	100	0.197
3.116-3.362	0.218	60	0.186	1006	0.188	1066	0.934	0.942	100	0.2
3.362-3.678	0.196	68	0.172	935	0.174	1003	0.952	0.957	100	0.192
3.678-4.104	0.232	36	0.167	860	0.17	896	0.942	0.955	100	0.19
4.104-4.724	0.209	42	0.147	768	0.151	810	0.958	0.968	100	0.17
4.724-5.749	0.138	34	0.179	635	0.177	671	0.965	0.961	99.7019	0.205
5.749-7.979	0.365	27	0.219	485	0.224	513	0.927	0.944	99.8051	0.252
7.979-29.394	0.21	17	0.164	302	0.167	320	0.961	0.967	99.6875	0.194

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	5.3203	-0.1306	0.3686	2.8176	-0.4473	5.886	-0.0522	0.0187	-0.2894	-0.006	-0.0541	-0.2156	0.4502	0.2039	0.1063	0.2121	0.1111	-0.007	0.0639	0.0098	0.079	27.6546	33.5871	16.8457
2	4.4787	1.1401	1.2017	3.3651	-1.0497	6.5764	-0.0971	-0.1542	0.0377	0.2838	-0.0187	-0.1997	0.2671	0.3125	0.1158	0.1548	0.1049	-0.0351	0.0867	-0.0124	0.0672	30.527	35.2768	23.4091
3	2.3561	-0.1044	0.8574	1.2042	0.5346	3.6116	0.0718	0.1455	-0.1214	-0.1176	0.0385	-0.0346	0.5548	0.1485	-0.1103	0.2295	0.0684	0.0082	0.0404	-0.001	0.0315	23.7802	32.258	7.4192
4	2.4314	0.054	0.405	1.4569	-0.7449	4.3517	0.0064	0.1634	-0.0343	-0.0938	0.0432	-0.0541	-0.0857	0.1056	-0.0496	0.1189	0.0403	-0.0054	0.0382	-0.0143	0.0086	20.5059	42.8005	6.1019
5	2.3578	0.58	0.5727	2.6083	0.489	4.2064	0.0564	-0.1075	-0.0412	-0.0247	0.0174	-0.0652	0.093	0.2629	-0.0738	0.1249	0.0589	-0.0234	0.0519	-0.0163	0.0426	23.4904	44.6655	19.8446
6	7.4614	-0.3886	3.4394	2.1193	-0.033	4.9438	-0.0785	0.2245	0.6151	0.2452	-0.1022	0.1942	-0.3933	-0.2656	0.1807	0.221	0.1155	-0.0387	0.1179	0.0135	0.1792	9.069	64.1853	11.6272
7	2.0674	-1.86	0.3278	2.323	0.012	6.8341	0.0248	0.116	0.2359	-0.2509	-0.1214	-0.1104	-0.3644	-0.0882	0.0966	0.2167	0.1005	-0.0294	0.0721	0.0091	0.0945	8.7	65.6355	9.9535
8	3.6467	-2.0812	0.1792	3.2908	-0.4837	3.5881	-0.3407	-0.3913	0.1207	0.4509	0.2912	-0.0476	-0.475	-0.2633	0.0495	0.237	0.1509	-0.0259	0.1115	-0.0141	0.0362	11.2808	59.9713	22.5698
9	2.8687	-0.3065	2.0415	1.1883	-1.5805	4.4486	-0.0141	0.0204	0.2268	0.136	-0.1266	-0.0455	-0.3269	0.2919	0.1408	0.1547	0.0387	-0.0017	0.0643	-0.0009	0.0643	22.3369	55.213	20.6785
10	3.409	0.5799	-0.5056	8.1723	-0.6659	2.4158	0.069	0.1726	0.03	-0.3262	-0.1018	0.1859	-0.2554	-0.1555	0.0328	0.108	0.0649	-0.012	0.0451	-0.0025	0.0292	13.5439	52.1261	7.8445

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	6 - 20
2	X-RAY DIFFRACTION	2	ALL	AAA	21 - 33
3	X-RAY DIFFRACTION	3	ALL	AAA	34 - 71
4	X-RAY DIFFRACTION	4	ALL	AAA	72 - 105
5	X-RAY DIFFRACTION	5	ALL	AAA	106 - 125
6	X-RAY DIFFRACTION	6	ALL	BBB	6 - 20
7	X-RAY DIFFRACTION	7	ALL	BBB	21 - 42
8	X-RAY DIFFRACTION	8	ALL	BBB	43 - 88
9	X-RAY DIFFRACTION	9	ALL	BBB	89 - 109
10	X-RAY DIFFRACTION	10	ALL	BBB	110 - 125

-
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