PDB-7el3: Crystal structure of HpaR-DNA complex from Acinetobacter baumannii

ID or keywords:

Entry

Database: PDB / ID: 7el3

Title

Crystal structure of HpaR-DNA complex from Acinetobacter baumannii

Components

Chains: C
Chains: D
Homoprotocatechuate degradation operon regulator HpaR

Keywords

DNA BINDING PROTEIN / MarR family of transcription regulators / Transcription factor in HPA-degradation pathway / Acinetobacter baumannii

Function / homology

Function and homology information

DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Acinetobacter baumannii ZW85-1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Permsirivisarn, P. / Pakotiprapha, D.

Funding support

Thailand, 2items

Citation

Journal: Febs J. / Year: 2022
Title: Mechanism of transcription regulation by Acinetobacter baumannii HpaR in the catabolism of p-hydroxyphenylacetate.
Authors: Permsirivisarn, P. / Yuenyao, A. / Pramanpol, N. / Charoenwattanasatien, R. / Suginta, W. / Chaiyen, P. / Pakotiprapha, D.

History

Deposition	Apr 7, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 22, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7el3.cif.gz	224.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7el3_validation.pdf.gz	456.3 KB	Display	wwPDB validaton report
Full document	7el3_full_validation.pdf.gz	459.1 KB	Display
Data in XML	7el3_validation.xml.gz	18.3 KB	Display
Data in CIF	7el3_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/el/7el3 ftp://data.pdbj.org/pub/pdb/validation_reports/el/7el3	HTTPS FTP

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Related structure data

Related structure data	7el2SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6x12-d 1hzu-d 4m2b-d 3nqp-2 4aij-d 2kb1-d 4lll-2 5nzg-d 6mon-2 1qom-2 Search similar-shape structures by Omokage search (details) 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Homoprotocatechuate degradation operon regulator HpaR

B: Homoprotocatechuate degradation operon regulator HpaR

C: Chains: C

D: Chains: D

hetero molecules

47.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	47.423, 55.150, 57.072
Angle α, β, γ (deg.)	81.135, 66.793, 67.965
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Homoprotocatechuate degradation operon regulator HpaR Mass: 16504.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: hpaR, EWO92_01730, EWO96_02085, EWP49_02085, FD887_17210 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Q4GPX4
#2: DNA chain	Chains: C Mass: 7076.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acinetobacter baumannii ZW85-1 (bacteria)
#3: DNA chain	Chains: D Mass: 7036.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acinetobacter baumannii ZW85-1 (bacteria)
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.7 Å³/Da / Density % sol: 54.42 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100 mM sodium HEPES; MOPS, pH 7.5, 20 mM DL-glutamic acid, 20 mM DL-alanine, 20 mM glycine, 20 mM DL-lysine, 20 mM DL-serine, 20 % (v/v) glycerol and 10 % (v/v) PEG 4000 PH range: 7.5

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 4, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→27.61 Å / Num. obs: 52505 / % possible obs: 96.9 % / Redundancy: 2.4 % / B_iso Wilson estimate: 19.27 Å² / CC_1/2: 1 / R_merge(I) obs: 0.022 / R_pim(I) all: 0.017 / R_rim(I) all: 0.028 / Net I/σ(I): 19.1
Reflection shell	Resolution: 1.7→1.73 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 2711 / CC_1/2: 0.994

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
Blu-Ice		data collection
DIALS		data reduction
PHASER		phasing
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7EL2

7el2

Resolution: 1.7→27.61 Å / SU ML: 0.1371 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.6244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1926	4914	4.77 %
R_work	0.1642	98087	-
obs	0.1657	52376	95.05 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→27.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2230	937	6	427	3600

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0092	3310
X-RAY DIFFRACTION	f_angle_d	1.2364	4645
X-RAY DIFFRACTION	f_chiral_restr	0.0641	532
X-RAY DIFFRACTION	f_plane_restr	0.0099	425
X-RAY DIFFRACTION	f_dihedral_angle_d	26.6757	750

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.72	0.2697	124	0.2336	3141	X-RAY DIFFRACTION	91.51
1.72-1.74	0.2383	155	0.2094	3176	X-RAY DIFFRACTION	91.56
1.74-1.76	0.2597	183	0.2164	3155	X-RAY DIFFRACTION	92.11
1.76-1.78	0.2307	154	0.2001	3186	X-RAY DIFFRACTION	93.04
1.78-1.81	0.2479	134	0.1967	3145	X-RAY DIFFRACTION	92.26
1.81-1.83	0.2096	138	0.192	3294	X-RAY DIFFRACTION	93.67
1.83-1.86	0.2149	150	0.1829	3209	X-RAY DIFFRACTION	92.94
1.86-1.89	0.2132	131	0.1775	3256	X-RAY DIFFRACTION	93.62
1.89-1.91	0.1953	140	0.1796	3275	X-RAY DIFFRACTION	94.28
1.91-1.95	0.1997	156	0.1765	3205	X-RAY DIFFRACTION	94.36
1.95-1.98	0.2285	181	0.1769	3316	X-RAY DIFFRACTION	94.41
1.98-2.02	0.2288	164	0.172	3134	X-RAY DIFFRACTION	94.5
2.02-2.05	0.2095	192	0.1698	3325	X-RAY DIFFRACTION	94.54
2.05-2.1	0.2281	146	0.1704	3197	X-RAY DIFFRACTION	95.13
2.1-2.14	0.1987	161	0.1642	3376	X-RAY DIFFRACTION	95.13
2.14-2.19	0.194	132	0.1663	3303	X-RAY DIFFRACTION	95.95
2.19-2.25	0.2208	171	0.1658	3265	X-RAY DIFFRACTION	95.18
2.25-2.31	0.1903	191	0.1648	3309	X-RAY DIFFRACTION	96
2.31-2.37	0.2014	202	0.1715	3322	X-RAY DIFFRACTION	96.23
2.37-2.45	0.2426	166	0.1681	3199	X-RAY DIFFRACTION	95.92
2.45-2.54	0.1837	139	0.1731	3349	X-RAY DIFFRACTION	96.51
2.54-2.64	0.2279	160	0.1846	3387	X-RAY DIFFRACTION	96.65
2.64-2.76	0.2432	144	0.1833	3346	X-RAY DIFFRACTION	97
2.76-2.91	0.2219	153	0.1856	3361	X-RAY DIFFRACTION	97.13
2.91-3.09	0.1946	167	0.1822	3278	X-RAY DIFFRACTION	97.26
3.09-3.33	0.1923	231	0.1659	3270	X-RAY DIFFRACTION	95.66
3.33-3.66	0.1685	228	0.1414	3332	X-RAY DIFFRACTION	97.91
3.66-4.19	0.1717	233	0.1304	3264	X-RAY DIFFRACTION	98.29
4.19-5.27	0.14	133	0.137	3476	X-RAY DIFFRACTION	98.5
5.27-27.61	0.1612	155	0.1569	3236	X-RAY DIFFRACTION	94.4

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	1.70851022961	-0.547370351064	-0.673834807765	4.50760044705	1.36307692391	3.01460559131	0.0166960404117	-0.0217293324014	0.106008717035	0.0537209668419	0.0860770064756	-0.362486651604	0.140769190578	0.0360142777901	-0.122104658244	0.180824502427	0.0255990036485	-0.0333999800636	0.137421960171	-0.0425129657449	0.197561176041	-1.60941890486	-7.72840762096	-4.80033308773
2	1.66631605235	-2.1533179911	-1.10696488702	5.21737233981	2.2838079665	2.54378281973	0.433824914105	0.228160662145	0.190881452084	-0.800853604579	-0.367775984792	-0.557942806672	-0.220268882002	-0.120000610845	-0.118858387211	0.351479733912	0.0778694199931	0.00151442931732	0.281474619584	-0.0110083876228	0.230197151009	1.34030310644	-18.1660478466	-22.7990091259
3	1.58440466803	-0.208807792189	0.168573685558	3.50328209848	0.418209997355	2.92914969759	-0.0857534654139	-0.0521852793521	-0.341232804605	-0.0416970591518	-0.336871258007	0.379425243251	0.718374682839	-0.0936936219289	0.0579463553544	0.247625610607	0.00358590416533	-0.00086955674238	0.216532516479	-0.0820409940454	0.457435940853	-19.7682602905	-13.6115496084	-6.24540197911
4	2.05530779856	-0.445115843756	0.968142925274	3.20650733994	0.873261086386	2.04724381574	0.0822997720732	0.115120186559	-0.00949964420299	-0.243276828338	-0.0497371618367	0.0457829851469	-0.0818535614497	-0.0399865732267	0.000348980452666	0.158860792512	0.0191804655913	-0.022704846178	0.121993972607	-0.0197325458335	0.138024754473	-12.7064762847	7.59689351691	-8.1718651055
5	4.68173980865	-2.83026134283	-2.29078813602	7.7893216817	5.13569035905	3.62935559198	0.321822328676	0.0929508820595	0.481853986466	-0.686467963855	0.064768420316	-0.418860053352	-0.94912291102	0.0529221624172	-0.326442297935	0.383259478876	-0.0092798647417	0.0310156326714	0.210412993378	0.0346461333288	0.366102683421	-7.90085737288	20.5487514154	-5.18461248336
6	1.70896442138	0.0567106232071	0.0927391787653	1.67870075971	0.612637051358	1.8081982251	0.0324821814717	0.258169154106	-0.194479812579	-0.382132236944	-0.0330273939599	0.0931211748812	-0.281547733012	-0.074017326156	0.0124692853039	0.241132486552	0.0982420693456	-0.0516345450413	0.202157410099	-0.0287059934395	0.291463052894	-19.0354974921	8.70219496032	-14.2320697729
7	7.69385481376	-0.046200991355	3.05869108748	1.48384207524	-0.227375174357	4.92606636045	-0.540341329486	-0.614657940861	0.294018544912	0.184481435097	0.096116373684	0.0860074648683	-0.589122007097	-0.404676354314	0.277554486677	0.212940725782	0.0617820973749	0.0208566883333	0.239714957499	-0.110702579193	0.476606587693	-30.2814735743	-4.12408554803	-1.8304308702
8	3.37255980377	-2.21433775363	3.11650703539	3.70977109528	-2.96485995551	3.52531730472	-0.14016415704	0.044242491068	0.0623584618817	0.297828404864	-0.0885666519835	0.369209159251	-0.350094860431	0.169193273419	0.216259043012	0.18159886375	-0.0070871574197	-0.0020450332846	0.191998960527	-0.0585890100476	0.355190431998	-20.2187486442	-4.27587238391	-0.490786347573
9	2.09955347187	-0.820843018434	-1.11760698755	4.64606981554	1.6316798079	2.51806476994	-0.196436079442	-0.223012234297	0.0924251958312	0.58741113258	0.0874242468241	0.221141726366	0.0882842933285	-0.0606443653895	0.0714012916024	0.269428501548	0.0462382114284	0.0100918756088	0.213008251039	-0.0035231470593	0.184229671952	-9.87356982987	-18.1003802369	4.26520699193
10	5.2099061093	0.407886191734	-1.41963067057	6.66076832086	0.139992789907	2.81350350992	-0.0883886787497	0.138833594269	-0.314291844117	-0.125504789168	-0.0140975892171	0.541784606455	0.310945726086	-0.271019844677	0.0231559364784	0.167329149406	0.0275240477573	-0.050569620685	0.134598986686	-0.0502830762586	0.18748690909	-9.43412886422	-23.6686877536	-9.05322726006
11	1.1798708229	-0.673062441481	-0.198252935357	3.86643557355	0.824359688172	2.93195772044	-0.00804753244181	-0.0284222987999	-0.124335136416	0.29328252058	0.0293354260925	0.00396935531665	0.171374051271	0.0617372987157	-0.0959401836316	0.170866218557	0.033596196052	-0.0466915732922	0.156208294543	-0.0218927876725	0.193704015941	0.0995553439222	-25.7800480204	-6.78379521005
12	3.59390812525	-4.24921324265	-0.233378139481	6.45697901771	0.339502222428	2.59772408566	-0.24920891065	-0.722337989196	-0.433431544362	0.865843871069	0.281125282499	0.805489618573	0.372527041626	-0.19126268014	0.00197577314891	0.539488485922	-0.0630893573081	0.144411545414	0.394575457371	0.00311524727185	0.380933309208	-16.5397870553	-19.9249040719	10.6484024019
13	4.82622679104	1.22016762989	-3.17045662634	3.20302289888	-2.76893715576	6.75395057385	-0.216421307752	0.432731131362	-0.443673202521	-0.465179929379	-0.0288881751813	0.223105952637	0.682911012954	-0.475172472614	0.344263197766	0.221498746765	-0.0257114530041	-0.0263519941853	0.202363936548	-0.0917580803319	0.607364209882	-29.2198272043	-14.280422909	-5.41763331843
14	0.829348124512	-0.658800915196	0.0163273403783	0.969232645513	-0.0301918517357	1.76891422998	0.288043259255	0.320599188857	-0.0929214970597	-0.362540147155	-0.0402711663785	-0.144769496108	-0.0344315663124	-0.176237345657	-0.102974418008	0.249185817558	0.0488943140315	0.00393281198849	0.224091833516	-0.0320754213535	0.163904302894	-0.0111147010041	-17.1802705716	-19.5586102504
15	0.319823467044	-0.556828305272	-0.0192118409256	3.35535254932	0.919147225835	0.41348941044	0.0117450020971	-0.170818495174	0.0641319357303	0.469383346651	0.141161484569	-0.475223211669	0.0599894836416	0.041839188106	-0.143146045874	0.23953131514	0.0205397710721	-0.0714433825673	0.240687386201	-0.059845119948	0.222401366873	-2.52325481174	7.38709647502	6.9065891468
16	0.530546750412	0.513140019881	1.23526507811	2.29143512821	1.48867048339	2.96999804887	-0.0356732076196	-0.20337498703	-0.0219692631667	0.56604515177	0.10008386171	-0.184163144017	0.102589779808	-0.14077287694	-0.0881463248133	0.358121854572	0.00183680507854	-0.0596657452865	0.247421330462	-0.0576016306224	0.247277156571	-2.70250795581	10.587405573	10.7598987787

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'C' and (resid 11 through 15 )	C	C	11 - 15
2	2	chain 'C' and (resid 16 through 23 )	C	C	16 - 23
3	3	chain 'A' and (resid 3 through 22 )	A	A	3 - 22	1 - 20
4	4	chain 'A' and (resid 23 through 74 )	A	A	23 - 74	21 - 72
5	5	chain 'A' and (resid 75 through 85 )	A	A	75 - 85	73 - 83
6	6	chain 'A' and (resid 86 through 120 )	A	A	86 - 120	84 - 118
7	7	chain 'A' and (resid 121 through 140 )	A	A	121 - 140	119 - 138
8	8	chain 'B' and (resid 6 through 22 )	B	B	6 - 22	1 - 17
9	9	chain 'B' and (resid 23 through 46 )	B	B	23 - 46	18 - 41
10	10	chain 'B' and (resid 47 through 61 )	B	B	47 - 61	42 - 56
11	11	chain 'B' and (resid 62 through 95 )	B	B	62 - 95	57 - 90
12	12	chain 'B' and (resid 96 through 120 )	B	B	96 - 120	91 - 115
13	13	chain 'B' and (resid 121 through 140 )	B	B	121 - 140	116 - 135
14	14	chain 'D' and (resid 1 through 10 )	D	E	1 - 10
15	15	chain 'D' and (resid 11 through 23 )	D	E	11 - 23
16	16	chain 'C' and (resid 1 through 10 )	C	C	1 - 10

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