PDB-7fib: Crystal structure of the regulatory domain of AceR in Acinetobact...

ID or keywords:

Entry

Database: PDB / ID: 7fib

Title

Crystal structure of the regulatory domain of AceR in Acinetobacter baumannii

Components

LysR family transcriptional regulator

Keywords

DNA BINDING PROTEIN / dimer / chlorhexidine resistance /

LTTR

Function / homology

Function and homology information

DNA-binding transcription factor activity
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Chi, P. / Guo, L.

Citation

Journal: To Be Published
Title: Crystal structure of the regulatory domain of AceR in Acinetobacter baumannii
Authors: Chi, P. / Guo, L.

History

Deposition	Jul 30, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 3, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7fib.cif.gz	182.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7fib.ent.gz	145.1 KB	Display	PDB format
PDBx/mmJSON format	7fib.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/fi/7fib ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fib	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: LysR family transcriptional regulator

B: LysR family transcriptional regulator

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: cross-linking, equilibrium centrifugation

Unit cell

Length a, b, c (Å)	125.215, 125.215, 61.580
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	LysR family transcriptional regulator Mass: 24988.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: AceR Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2G1TN50
#2: Chemical	ChemComp-BR / BROMIDE ION / Bromide Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.89 % / Description: Diamond-shaped
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% (w/v) polyethylene glycol 4000, 0.05M sodium cacodylate trihydrate pH 6.0, 0.1M sodium chloride, 0.0005M spermine PH range: 5.6-6.2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.919 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.919 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 62595 / % possible obs: 100 % / Redundancy: 12.2 % / B_iso Wilson estimate: 52.55 Å² / R_merge(I) obs: 0.059 / R_pim(I) all: 0.012 / R_rim(I) all: 0.06 / Χ²: 0.516 / Net I/σ(I): 5.5

Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²
2.1-2.14	9.85	1.557	1599	0.69	0.352	1.598	0.414
2.14-2.18	11.15	1.325	1609	0.812	0.283	1.356	0.416
2.18-2.22	12.2	1.197	1600	0.866	0.246	1.222	0.413
2.22-2.26	12.25	0.985	1593	0.917	0.2	1.006	0.418
2.26-2.31	12.5	0.76	1611	0.954	0.154	0.775	0.417
2.31-2.37	12.15	0.608	1621	0.968	0.125	0.621	0.427
2.37-2.42	11.5	0.503	1571	0.974	0.107	0.514	0.452
2.42-2.49	12.9	0.402	1625	0.985	0.081	0.41	0.454
2.49-2.56	13.1	0.324	1610	0.99	0.064	0.33	0.46
2.56-2.65	13	0.229	1586	0.994	0.046	0.234	0.457
2.65-2.74	12.7	0.185	1622	0.996	0.037	0.189	0.461
2.74-2.85	12.45	0.15	1609	0.996	0.031	0.153	0.493
2.85-2.98	11.4	0.109	1610	0.998	0.023	0.112	0.502
2.98-3.14	12.9	0.082	1613	0.999	0.016	0.083	0.531
3.14-3.33	12.9	0.062	1603	0.999	0.012	0.063	0.576
3.33-3.59	12.8	0.05	1625	1	0.01	0.051	0.62
3.59-3.95	11.65	0.041	1616	1	0.009	0.042	0.675
3.95-4.52	13.1	0.036	1631	1	0.007	0.036	0.688
4.52-5.7	12.05	0.035	1639	1	0.007	0.035	0.672
5.7-50	12.6	0.034	1686	1	0.007	0.035	0.733

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→24.88 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2309	3904	6.24 %
R_work	0.2052	58691	-
obs	0.2068	62595	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 195.75 Å² / B_iso mean: 60.0339 Å² / B_iso min: 31.94 Å²

Refinement step

Cycle: final / Resolution: 2.1→24.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3317	0	5	62	3384
B_iso mean	-	-	169.53	59.92	-
Num. residues	-	-	-	-	410

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.13	0.3128	140	0.3094	2102	2242	97
2.13-2.15	0.3192	136	0.3041	2099	2235	100
2.15-2.18	0.3055	136	0.2855	2088	2224	100
2.18-2.21	0.3251	146	0.2824	2126	2272	100
2.21-2.24	0.2799	138	0.2888	2112	2250	100
2.24-2.28	0.3628	140	0.2773	2126	2266	100
2.28-2.31	0.3098	136	0.2785	2083	2219	100
2.31-2.35	0.2723	142	0.2622	2083	2225	100
2.35-2.39	0.3537	140	0.2724	2103	2243	100
2.39-2.43	0.2711	134	0.2446	2110	2244	100
2.43-2.48	0.2962	146	0.2543	2129	2275	100
2.48-2.53	0.2331	132	0.256	2110	2242	100
2.53-2.59	0.2867	138	0.2491	2095	2233	100
2.59-2.65	0.2342	140	0.2433	2104	2244	100
2.65-2.71	0.2881	144	0.2516	2120	2264	100
2.71-2.79	0.2957	154	0.2541	2146	2300	100
2.79-2.87	0.3114	136	0.2456	2017	2153	100
2.87-2.96	0.3073	140	0.2428	2126	2266	100
2.96-3.07	0.2957	144	0.2409	2112	2256	100
3.07-3.19	0.2753	142	0.2474	2105	2247	100
3.19-3.33	0.2615	132	0.2097	2107	2239	100
3.33-3.51	0.2402	138	0.2059	2088	2226	100
3.51-3.73	0.2294	140	0.1859	2081	2221	99
3.73-4.01	0.2149	137	0.183	2108	2245	99
4.01-4.42	0.1657	127	0.1602	2093	2220	99
4.42-5.05	0.198	145	0.1579	2079	2224	99
5.05-6.35	0.2182	135	0.1931	2066	2201	98
6.35-24.88	0.1543	146	0.1743	1973	2119	94

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	2.4495	1.2249	0.1853	2.6573	-2.5693	5.512	-0.195	-0.0542	-0.2623	0.1571	-0.1561	-0.1414	0.0157	-0.2094	0.0749	0.286	0.0305	-0.0621	0.3643	-0.0715	0.3986	-2.5669	48.3132	23.1892
2	1.7779	-0.6356	1.1046	1.1324	1.0843	2.705	-0.1405	-0.1076	0.3874	-0.2393	-0.0158	-0.1104	-0.2571	0.4043	0.0428	0.3393	-0.0057	0.0227	0.4055	0.0221	0.4904	1.8499	55.1482	18.6495
3	2.8566	0.6495	0.1835	0.9184	0.5298	2.0532	0.8407	0.8832	-0.2078	-1.0104	-1.3785	0.0702	-0.3633	0.2414	0.06	0.4311	0.1035	0.0256	0.6903	0.0177	0.3251	7.9384	42.9479	-6.1184
4	3.7461	0.0925	0.0368	0.468	0.1194	2.0702	-0.039	-0.0497	-0.0227	-0.078	-0.0161	-0.1132	0.3299	0.323	0.0626	0.3758	0.069	0.0182	0.4109	-0.0084	0.3352	5.0417	42.1549	1.399
5	1.3985	0.048	1.5071	0.5538	-0.4159	1.6315	-0.0663	-0.1266	0.1751	0.1022	0.1974	-0.2134	-0.0833	0.3551	-0.0344	0.3291	0.0556	0.0075	0.4429	-0.0626	0.4483	8.1531	53.4768	28.0821
6	3.0427	-1.6327	-0.6511	2.1384	1.6422	2.8778	-0.1404	-0.1374	-0.0044	-0.0986	0.0697	0.1663	0.5249	0.5911	0.0028	0.2804	-0.0385	-0.064	0.3118	0.0424	0.3469	-10.9426	47.0908	-4.0659
7	2.9271	-0.202	0.5617	1.6401	0.5071	3.2329	-0.0157	0.0013	0.5309	0.028	0.0246	0.0304	-0.5632	-0.2042	0.0065	0.3391	-0.0154	-0.0141	0.3596	0.0572	0.4047	-14.9496	56.7659	-0.7818
8	0.0282	-0.269	-0.6152	1.5509	-2.1216	3.0492	-0.032	0.1974	-0.1472	-0.4672	0.1583	0.4099	0.4807	-0.5067	0.1463	0.4904	-0.1467	-0.1109	0.5176	-0.0308	0.4675	-22.1329	43.6643	4.6285
9	3.3256	1.2079	-0.2661	0.7122	1.0286	2.7407	0.3142	-0.3931	-0.1535	0.643	-0.3753	0.112	0.0438	0.0023	0.0473	0.406	-0.0899	0.0059	0.3962	0.0187	0.3425	-19.2994	39.2828	25.23
10	3.4139	1.5726	-0.4596	1.6107	-0.7393	3.1317	-0.006	0.0128	-0.0813	-0.0641	0.0166	-0.0533	0.3626	-0.2592	0.0214	0.3221	-0.0272	-0.0172	0.3208	0.0195	0.3128	-16.3664	39.0039	17.834
11	1.4088	-0.6783	0.0405	1.6471	1.6512	1.3633	0.0543	0.1884	-0.1248	0.1938	-0.0949	-0.1132	-0.9486	-1.058	0.0776	0.4892	0.0558	-0.0194	0.5276	0.0522	0.4407	-21.2333	53.794	-2.931
12	3.4251	1.2188	0.4284	1.7029	0.5394	0.0255	-0.4482	0.7357	-0.0128	-0.52	0.5994	0.1402	-0.2299	0.0672	-0.0056	0.4316	-0.1338	-0.0769	0.6141	0.1491	0.3825	-23.4186	46.2664	-14.4713

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 33 )	A	8 - 33
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 88 )	A	34 - 88
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 89 through 118 )	A	89 - 118
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 119 through 177 )	A	119 - 177
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 212 )	A	178 - 212
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 8 through 33 )	B	8 - 33
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 34 through 72 )	B	34 - 72
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 73 through 88 )	B	73 - 88
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 89 through 118 )	B	89 - 118
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 119 through 177 )	B	119 - 177
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 178 through 193 )	B	178 - 193
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 194 through 212 )	B	194 - 212

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