PDB-7mx5: Crystal structure of TolB from Acinetobacter baumannii

ID or keywords:

Entry

Database: PDB / ID: 7mx5

Title

Crystal structure of TolB from Acinetobacter baumannii

Components

Tol-Pal system protein TolB

Keywords

TRANSPORT PROTEIN / structural genomics / CSGID / Center For Structural Genomics Of Infectious Disease / NIAID / National Institute Of Allergy And Infectious Diseases / TOL / TOLB / TOL-PAL COMPLEX / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

protein import / periplasmic space / cell cycle / cell division
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.42 Å

Authors

Stogios, P.J. / Evdokimova, E. / Endres, M. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

Canada, 1items

Citation

Journal: To Be Published
Title: Crystal structure of TolB from Acinetobacter baumannii
Authors: Stogios, P.J.

History

Deposition	May 18, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mx5.cif.gz	371.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7mx5.ent.gz	268.3 KB	Display	PDB format
PDBx/mmJSON format	7mx5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mx5_validation.pdf.gz	434.1 KB	Display	wwPDB validaton report
Full document	7mx5_full_validation.pdf.gz	444.6 KB	Display
Data in XML	7mx5_validation.xml.gz	32.3 KB	Display
Data in CIF	7mx5_validation.cif.gz	45.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mx/7mx5 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/7mx5	HTTPS FTP

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Related structure data

Related structure data	2w8bS S: Starting model for refinement
Similar structure data	1c5k-d 4a9o-d 4a9j-d 4a9n-d 1x0j-d 4de8-d 6db0-d 6k05-d 3iax-d 2dvs-d 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: IDP97707

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #225 - Sep 2018 Phytase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Tol-Pal system protein TolB

B: Tol-Pal system protein TolB

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

1

A: Tol-Pal system protein TolB

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

2

B: Tol-Pal system protein TolB

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

Unit cell

Length a, b, c (Å)	43.498, 98.443, 83.832
Angle α, β, γ (deg.)	90.000, 92.072, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Tol-Pal system protein TolB Mass: 43856.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (ATCC 19606) (bacteria) Strain: ATCC 19606 / Gene: tolB, ATCC19606_08470, FQU82_02953 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: A0A6F8TCJ6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Tol-Pal system protein TolB

Mass: 43856.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acinetobacter baumannii (ATCC 19606) (bacteria)
Strain: ATCC 19606 / Gene: tolB, ATCC19606_08470, FQU82_02953 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: A0A6F8TCJ6

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 39.89 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.1 M sodium/potassium tartrate, 0.1 M Tris pH 8.5, 2% (w/v) PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 22, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.42→30 Å / Num. obs: 26751 / % possible obs: 98.8 % / Redundancy: 3.5 % / B_iso Wilson estimate: 39.06 Å² / R_merge(I) obs: 0.085 / R_pim(I) all: 0.052 / Net I/σ(I): 10.63
Reflection shell	Resolution: 2.42→2.46 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.458 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 1131 / CC_1/2: 0.708 / R_sym value: 0.349 / % possible all: 84.7

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
BALBES		phasing
ARP/wARP		model building
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2W8B

2w8b

Resolution: 2.42→29.63 Å / SU ML: 0.3105 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2437	1343	5.02 %
R_work	0.1937	25386	-
obs	0.1963	26729	98.67 %

Solvent computation

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

Displacement parameters

B_iso mean: 51.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.42→29.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6174	0	0	302	6476

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	6337
X-RAY DIFFRACTION	f_angle_d	0.6666	8611
X-RAY DIFFRACTION	f_chiral_restr	0.0607	944
X-RAY DIFFRACTION	f_plane_restr	0.0049	1148
X-RAY DIFFRACTION	f_dihedral_angle_d	17.6856	2385

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 (%)
2.42-2.5	0.3551	117	0.2755	2216	X-RAY DIFFRACTION	87.81
2.5-2.6	0.3535	135	0.2774	2539	X-RAY DIFFRACTION	98.93
2.6-2.72	0.3378	133	0.2572	2585	X-RAY DIFFRACTION	99.89
2.72-2.86	0.2662	138	0.2421	2551	X-RAY DIFFRACTION	100
2.86-3.04	0.312	132	0.2283	2548	X-RAY DIFFRACTION	100
3.04-3.28	0.281	144	0.2155	2577	X-RAY DIFFRACTION	100
3.28-3.61	0.2278	130	0.1823	2585	X-RAY DIFFRACTION	100
3.61-4.13	0.2219	136	0.1678	2566	X-RAY DIFFRACTION	100
4.13-5.2	0.1727	140	0.1405	2591	X-RAY DIFFRACTION	100
5.2-29.63	0.2295	138	0.1843	2628	X-RAY DIFFRACTION	99.96

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	6.67943004965	-0.266852522808	-3.75348307215	4.57743348853	1.24869065557	4.58563747313	0.211727659372	-0.296195227594	1.05780923659	0.218971184685	-0.019729695161	0.374021255658	-0.0673898547997	0.166970547064	-0.196015163737	0.437985068297	-0.00618691113738	0.0263503803123	0.301189142403	-0.115743212634	0.492323469209	1.84827760645	71.0872273534	84.4326147062
2	3.64873255691	2.19134027067	-0.616634332134	3.3084422847	0.16853815668	0.304529549497	0.0882180476214	0.0445722878902	0.271002400985	0.20670062714	0.0778926552182	0.273147026954	-0.0682789785796	-0.0789055380356	-0.178276538506	0.254110384905	0.0452791100683	-0.0350660830885	0.254374149712	0.0544415189748	0.230442132872	-10.690846403	50.6732611371	78.7424726544
3	4.44134305198	0.0271976952688	1.1765559593	4.99792689511	0.0322826092071	2.97866962103	-0.0805531027397	-0.247168763253	-0.0588279721688	-0.185757856652	0.0892445668628	-0.0287318610725	0.13475985851	-0.462841561495	0.0117308223934	0.259222018611	0.028483619253	0.0188046039996	0.399585562266	0.0698544658193	0.226957817972	-23.752842609	44.9358375678	66.1658602821
4	8.76635695479	-4.04255688096	-2.12084038719	8.90223038229	-2.67721059322	5.96224987058	-0.320298096892	0.639844749056	-0.403754122994	-0.831848601743	0.358649243316	1.00959620712	0.553074194895	-0.80741715304	-0.0906122106766	0.347010057258	-0.105814442765	-0.00253679809481	0.526092063459	0.0255855636165	0.37575176439	-18.876813147	43.7444149801	54.4053078232
5	5.78822552046	-3.88080270636	3.29994125597	4.19621755037	-0.47035165333	3.77469307081	0.357248243578	0.114157418559	0.422872840623	-1.53885240424	-0.256576624263	0.521176352713	-0.293330801447	-0.719017020071	-0.0546461366205	0.532311958613	0.0751304078169	0.113182824216	0.728408671734	0.200409281044	0.66718030299	-23.3372690861	47.5285620873	51.0078802752
6	8.47707170064	-5.65147928687	4.88929684586	6.95546713525	-5.26182307721	7.52442993736	-0.246191652967	0.196089016497	-1.48512439101	-0.828318649952	1.518728375	0.258890537095	1.19628662809	-1.36242390548	-1.24390094725	0.67162577018	-0.226561608449	-0.128043503685	0.832434150721	-0.139276936365	1.02243970148	-12.7330650565	35.8668614085	51.9842619626
7	2.62438863984	-1.25285352573	-0.125677046586	6.6956732373	-1.42249076354	6.82440191661	0.0820975783272	-0.0396566271648	0.135395098726	-0.00442660841686	0.000264590986752	-0.208720806876	-0.161078829463	-0.00669072426171	-0.0780187758952	0.167904236794	-0.0163636248551	-0.00406757348838	0.2474379894	-0.02834127702	0.242519003807	-4.48451630627	43.5100996633	52.4633148949
8	7.04267963789	2.75915790247	-0.539215101475	6.04816256362	-0.686543845413	7.66337433944	0.149779927268	0.318408116728	-1.47153717817	-0.331980450715	-0.237710673725	-0.868745542132	1.69774576612	0.899737506018	0.152109752914	0.502901771505	0.0939703790314	-0.0100421273161	0.281834949764	-0.0857246859398	0.504533175621	2.23696380951	35.1668049354	62.4013290219
9	2.62977331646	0.623505579044	0.226326523019	2.01042079544	-0.840053689937	3.76763152307	0.00610048436279	0.0352195571873	-0.161473355756	0.117773813069	-0.165714312725	-0.204495188182	-0.00524504061708	0.366070767187	0.156081172962	0.275676851118	0.0238484216347	0.0113918719802	0.319366475346	0.0346694262431	0.341359743061	0.97790063706	42.8449854185	70.3235346349
10	8.29410621944	-0.301114208136	-1.55515747691	8.35260706534	1.60868552496	3.93550404101	0.331092858308	-0.598373617079	-0.331289164835	-0.37231766649	-0.934421667986	-0.241429585311	0.242365777752	-0.0774012617697	0.582757020633	0.140379663227	-0.0207766620895	-0.0436187267145	0.456480183543	-0.0250551683273	0.244685725818	-10.6533468449	43.0700304029	75.8426025977
11	3.22401902871	0.218411144531	-1.06297703918	7.38408736965	-3.21523213184	3.3889132033	0.059357079031	-0.264321085609	0.278361090486	0.384693274218	0.0182778097213	0.223383847227	-0.229334793831	0.135530698346	-0.0892161009639	0.254039338142	-0.0155562766019	0.0141918898523	0.258340187514	-0.112418347605	0.288589069352	-2.85478953149	25.3299500672	45.4212858734
12	3.39237657598	1.9039949673	-1.23631115218	3.58870082415	-0.821088649408	1.53685445875	0.00822697486615	-0.234584425128	-0.263937274086	0.0460906185743	-0.0387631011346	-0.00380951806476	0.105952395106	-0.0274811235565	0.00674726593386	0.274608783597	0.0168382229672	-0.0274046988105	0.266861449522	0.004266102264	0.253197495377	0.0326953076677	17.8387391539	44.0340170006
13	3.42580899095	-0.728044364076	-1.14373724622	2.1476535723	0.718689579663	5.76987501262	0.117325495173	-0.0416490611149	0.278638478122	-0.192729420528	0.0602475022224	0.0585371817101	-0.116216148134	0.484345703433	-0.134750894218	0.204368971248	-0.00455501603302	0.00387879348619	0.203998819714	-0.00610391827291	0.308047728088	21.9457205325	34.2324383866	26.2626410516
14	7.37365453653	1.64478009422	0.980215041964	2.126542144	0.364560989944	7.49892996877	0.114048997957	0.376830459424	1.20090193696	-0.0629134992812	0.00395944500764	0.166063703316	-1.44392936666	-0.349879563995	-0.0663238427078	0.577172541254	0.0954693500306	0.119128054757	0.345064215944	0.0590047633352	0.523843636144	20.1784850519	38.0646931528	9.59189331978
15	5.3215339305	-0.350679866942	-2.28252179729	4.54759413162	1.38188348453	7.81427470934	0.217400777241	0.140456078595	0.0618275013581	-0.38346231852	-0.182217960635	0.394262702837	-0.399956251456	-0.34520769136	-0.027911819669	0.278921897432	0.0101076765499	-0.0813982635191	0.307273527696	0.0315559564759	0.271206210255	3.75386897135	37.9561199191	13.1096519078
16	6.11186151043	-1.1671146786	-0.365297848514	2.46561843661	-0.116502892885	2.88860523003	0.223295149546	0.00541025788192	-0.0420662353633	-0.0104621087576	-0.157547483422	0.128602099885	-0.0391783944225	-0.0815863112232	-0.0633201063925	0.2341791799	0.00127616005949	0.000939304671015	0.183059775376	0.00271499396086	0.249844057055	2.10942392147	37.6708457933	29.9529065272
17	2.84095966203	-1.31494527435	0.626468702316	5.61449130071	0.942455243865	6.78917702641	1.32906579716	0.106677585887	-0.311830449272	0.412126067944	-0.902702015579	-1.07014731057	-0.103590282178	0.980319406235	-0.353003530789	0.397798179277	0.0103538361235	-0.0679672215967	0.447057117952	0.0169653560986	0.424606684673	3.31581810838	46.7711334279	82.7585558774
18	8.59790652733	1.61418709076	-0.271054253768	2.18760322016	1.61892319054	7.07350069944	0.102811893371	-1.35942890625	-0.110221056894	0.297497864399	-0.181983659323	-0.201076020257	0.542143152357	0.415714592116	0.0869899789267	0.349513791407	0.0214217801864	0.00355324134855	0.439211933006	-0.00851100334409	0.422535726226	4.93186619015	61.1056588742	89.7739674132
19	6.81184743141	-1.68077348117	-4.80316002785	6.61845848269	1.09355607996	8.38062459586	0.102357294483	-1.19507020378	0.583095296228	0.44780177547	0.0359504232753	-0.0574668452482	-0.457617013544	1.18245775138	-0.131685566027	0.474690160629	-0.11546211039	0.0560507008433	0.465118169668	-0.0401194987503	0.347218389377	7.40314158569	69.8408651751	90.4018302904

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 'A' and (resid 109 through 135 )	A	A	109 - 135	83 - 109
2	2	chain 'A' and (resid 136 through 194 )	A	A	136 - 194	110 - 168
3	3	chain 'A' and (resid 195 through 246 )	A	A	195 - 246	169 - 220
4	4	chain 'A' and (resid 247 through 265 )	A	A	247 - 265	221 - 239
5	5	chain 'A' and (resid 266 through 278 )	A	A	266 - 278	240 - 252
6	6	chain 'A' and (resid 279 through 288 )	A	A	279 - 288	253 - 262
7	7	chain 'A' and (resid 289 through 340 )	A	A	289 - 340	263 - 314
8	8	chain 'A' and (resid 341 through 353 )	A	A	341 - 353	315 - 327
9	9	chain 'A' and (resid 354 through 412 )	A	A	354 - 412	328 - 386
10	10	chain 'A' and (resid 413 through 426 )	A	A	413 - 426	387 - 400
11	11	chain 'B' and (resid 28 through 71 )	B	B	28 - 71	1 - 44
12	12	chain 'B' and (resid 72 through 175 )	B	B	72 - 175	45 - 148
13	13	chain 'B' and (resid 176 through 259 )	B	B	176 - 259	149 - 232
14	14	chain 'B' and (resid 260 through 288 )	B	B	260 - 288	233 - 261
15	15	chain 'B' and (resid 289 through 353 )	B	B	289 - 353	262 - 326
16	16	chain 'B' and (resid 354 through 426 )	B	B	354 - 426	327 - 399
17	17	chain 'A' and (resid 27 through 41 )	A	A	27 - 41	1 - 15
18	18	chain 'A' and (resid 42 through 81 )	A	A	42 - 81	16 - 55
19	19	chain 'A' and (resid 82 through 108 )	A	A	82 - 108	56 - 82

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Open data

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Download

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Validation report

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Assembly

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About Yorodumi

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi