PDB-7tj1: Crystal Structure of the Putative Fluoride Ion Transporter CrcB B...

ID or keywords:

Entry

Database: PDB / ID: 7tj1

Title

Crystal Structure of the Putative Fluoride Ion Transporter CrcB Bab1_1389 from Brucella abortus

Components

Putative fluoride ion transporter CrcB

Keywords

UNKNOWN FUNCTION / fluoride ion transporter / camphor resistant protein / protein of unkown function / / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Metal binding protein

Function / homology

Function and homology information

inorganic anion transmembrane transporter activity / plasma membrane => GO:0005886
Similarity search - Function

Biological species

Brucella abortus 2308 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Kim, Y. / Tesar, C. / Pastore, T. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the Putative Fluoride Ion Transporter CrcB Bab1_1389 from Brucella abortus
Authors: Kim, Y. / Tesar, C. / Pastore, T. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 14, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 26, 2022	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7tj1.cif.gz	247.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7tj1.ent.gz	173.4 KB	Display	PDB format
PDBx/mmJSON format	7tj1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7tj1_validation.pdf.gz	781.6 KB	Display	wwPDB validaton report
Full document	7tj1_full_validation.pdf.gz	783 KB	Display
Data in XML	7tj1_validation.xml.gz	20.1 KB	Display
Data in CIF	7tj1_validation.cif.gz	27.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/7tj1 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/7tj1	HTTPS FTP

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Related structure data

Similar structure data	2oa8-d 1nfp-1 4j2f-1 1fvp-d 1qdu-3 4mdc-1 2xj9-d 3mxi-d 5kej-d 7a79-d 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: IDP95980

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative fluoride ion transporter CrcB

B: Putative fluoride ion transporter CrcB

C: Putative fluoride ion transporter CrcB

D: Putative fluoride ion transporter CrcB

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	89.955, 92.244, 63.405
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Putative fluoride ion transporter CrcB Mass: 16801.236 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Strain: 2308 / Gene: crcB, BAB1_1389 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q2YQP2

#1: Protein

Putative fluoride ion transporter CrcB

Mass: 16801.236 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Brucella abortus 2308 (bacteria) / Strain: 2308 / Gene: crcB, BAB1_1389 / Plasmid: pMCSG68 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q2YQP2

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Non-polymers , 6 types, 69 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-F / FLUORIDE ION Mass: 18.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.21 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M calcium acetate. 35 % PEG400, 0.1 sodium acetate pH 4.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97914 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 5, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 30127 / % possible obs: 95.7 % / Redundancy: 7.3 % / B_iso Wilson estimate: 40.47 Å² / R_merge(I) obs: 0.125 / Net I/σ(I): 16.6
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.659 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 1135 / CC_1/2: 0.75 / % possible all: 73.9

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 2.1→45.18 Å / SU ML: 0.2693 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8168
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2366	1548	5.15 %
R_work	0.1972	28512	-
obs	0.1991	30060	95.63 %

Solvent computation

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

Displacement parameters

B_iso mean: 48.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→45.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3880	0	41	57	3978

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	3973
X-RAY DIFFRACTION	f_angle_d	0.5077	5373
X-RAY DIFFRACTION	f_chiral_restr	0.0399	633
X-RAY DIFFRACTION	f_plane_restr	0.0043	685
X-RAY DIFFRACTION	f_dihedral_angle_d	10.8787	1418

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 (%)
2.1-2.17	0.3186	102	0.3056	1988	X-RAY DIFFRACTION	74.62
2.17-2.25	0.3034	101	0.2771	2297	X-RAY DIFFRACTION	84.88
2.25-2.34	0.2687	157	0.2591	2503	X-RAY DIFFRACTION	94.49
2.34-2.44	0.2649	170	0.2368	2631	X-RAY DIFFRACTION	98.94
2.44-2.57	0.2312	167	0.212	2643	X-RAY DIFFRACTION	99.89
2.57-2.73	0.2704	129	0.2034	2701	X-RAY DIFFRACTION	99.75
2.73-2.94	0.2447	157	0.2063	2681	X-RAY DIFFRACTION	99.93
2.94-3.24	0.2313	150	0.1875	2699	X-RAY DIFFRACTION	99.89
3.24-3.71	0.2475	137	0.1801	2724	X-RAY DIFFRACTION	99.65
3.71-4.67	0.2018	135	0.165	2770	X-RAY DIFFRACTION	99.93
4.67-45.18	0.2284	143	0.198	2875	X-RAY DIFFRACTION	99.21

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	4.12823765415	0.21043697724	0.123609089071	5.28457647202	-0.38497342163	4.54079325909	0.0587569277034	0.656980152283	-0.32581707014	-0.772715600263	0.190168803068	-0.329387858323	0.655413270466	0.223646365153	-0.217336096752	0.467217714609	0.0884715562042	-0.0462263546032	0.539409653826	-0.0996141646603	0.328666958496	7.94178651172	15.8670512889	7.22188663439
2	3.05016426946	-0.0251725713586	0.940810844788	4.49541237198	1.30181690483	2.60175465746	0.174715550804	1.0725080509	-0.272098560154	-0.744830513786	0.00457288845515	-0.586398785123	-0.132585937949	0.0963064377473	-0.265119545496	0.513813917749	-0.0904036704186	0.0641609096621	0.675735798863	-0.0303601068038	0.399507980225	10.6656611706	36.1619585652	3.884098649
3	3.14751092674	0.175510267492	0.919157579368	2.06851769924	-1.06576623083	2.55742518672	-0.374565639905	0.231466886143	0.443811303367	-0.0902974088408	0.509387508345	-0.946083013371	0.170170274264	0.387838793917	-0.227151812209	0.387983013956	0.00542953866936	-0.00436893119424	0.730744433686	-0.0695181905976	0.494761085562	18.3344114951	28.4520067562	12.2090636126
4	2.17479551395	-1.49183354612	-1.49286792329	5.6108828602	0.466059188569	5.39580687377	-0.772802662414	-1.02332603763	-0.920129694656	1.00968856568	0.285898743928	-0.0422964668358	0.778037395095	0.0201492979777	0.185782437238	0.476603815579	0.0279104770303	-0.0987161946589	0.67078565286	0.0538908098485	0.566375355732	4.53865453982	9.02513180857	42.996315154
5	3.90882056588	4.22498258954	5.39991693372	7.08787497395	4.75212432422	8.23070304477	0.497504896308	0.122960877738	-0.617462261809	-0.29276341169	-0.179757254317	-0.647632706118	-0.278207700393	0.324744759011	-0.271601591389	0.379953885297	-0.0303257082053	0.0223045105197	0.428266360739	-0.094018476432	0.485004418999	3.71575816435	8.91650935254	28.0880315356
6	4.69874617107	1.21962756413	0.926574167446	3.07647591878	1.43068972795	4.33108021519	-0.178481580744	0.262186245634	0.184437051413	-0.270184515004	0.194127344833	-0.308947115642	-0.494960003324	0.52292311477	-0.0548199430062	0.34383884057	-0.037923258348	0.0350638366882	0.508833169194	-0.0154416749068	0.365000265484	3.80165665436	21.0179374281	32.1978569251
7	4.62111921085	-0.867948795092	-0.926508045409	2.45899688483	0.0543724799525	2.54426968183	-0.123125103431	-0.25118755211	-0.277234491009	0.144888366949	0.161385669166	0.155458572322	0.228989505952	-0.0774209875303	-0.0810611619934	0.350878153725	-0.00181920384174	0.00356641688359	0.301278915915	-0.00912388013648	0.288637022975	-7.7214003864	14.4862834928	38.4433608634
8	6.8791902247	2.56285702579	-1.01586343047	2.79592764453	0.0410839154907	3.53171936568	0.189653465465	-0.828317375051	-0.731649762127	0.23012201916	-0.156976850718	0.287573094875	0.473023008289	-0.15322257248	0.0703810476094	0.421304587815	-0.0339756837394	-0.00642195691135	0.40376495496	0.0585562282182	0.483868617282	-7.04010577563	4.58306999749	35.4097090674
9	6.09910020352	-4.11342560942	3.5209502916	9.41987629535	-5.51974196561	3.56306213169	-0.487936981684	-0.391101135396	-0.273098654416	0.909601711216	0.93133709722	0.752308628764	-0.886655114151	-1.51382575312	-0.516243379377	0.362125814085	0.0861205335942	0.0351585076522	0.580770429022	-0.0262773405973	0.394935305344	-19.6623989476	30.8791356775	40.088273556
10	4.55180311082	0.547277404738	-0.0364432298751	4.72023562973	-0.124844902364	1.31048228312	0.0174573799612	0.361740527038	0.133764072712	-0.474876024089	-0.123939339645	-0.13097603223	-0.289217335418	-0.24132546122	0.0368396628873	0.416035756135	0.0196724380276	-0.000473210767852	0.552323396785	0.0480891902673	0.276584947693	-11.9024682827	29.4294608358	28.3157967701
11	5.00802374779	-0.707361495124	0.447805796892	1.60253214934	-0.0154748801994	3.19280065626	0.020222227621	0.00880585158449	0.114357256855	0.131890088563	0.0685133841477	-0.0652345742693	-0.0882124051493	0.342827784012	-0.0383307786573	0.358343120343	-0.0337285656786	0.0177556448546	0.348607987815	-0.0278292689723	0.317609566903	-6.94745783693	26.3756569718	40.6106564044
12	7.70920030958	-1.19975897997	6.09684389728	1.67846577146	-2.27000691274	7.22912354806	0.00172778048291	-0.378877152809	0.704441404402	0.0979547120127	-0.214079113238	-0.18935926502	-0.0546510041433	-0.0201107238946	0.190990187164	0.434128557986	-0.0504738047933	-0.00140087011582	0.372607917871	-0.116124323085	0.446014435018	-7.01303244207	36.0747174358	44.2403476986
13	5.67044681073	-2.1553432123	-4.05059969596	4.60212478277	2.36998925316	3.13759440974	0.673493301806	0.844922221039	0.682724829441	-0.541052687525	-0.258456622156	-0.0451722057407	-1.04794864875	-0.837508952049	-0.356806510235	0.465706431953	0.0482781711228	-0.0269004656308	0.464114723678	0.116004342079	0.534937920834	-6.05860334358	42.9888335547	7.32641419535
14	4.68420615404	0.0168860782344	-0.117719827056	5.10654472199	-0.591556548971	2.47915974472	0.0391290441274	-0.319039999353	0.0123043845184	0.556178599194	-0.0255131393451	0.111747137737	-0.211656841124	-0.467996495937	-0.0134467805201	0.376947551443	0.0167535507219	0.0234527010036	0.41560061885	0.0213098391646	0.22668613191	-5.57472305958	35.4113017172	19.0952107988
15	1.29448420128	-0.333646527263	0.252543181976	3.49415496095	-0.372153858526	2.42931126524	0.0547476182927	0.263798630644	0.00401925943514	0.0774985545078	-0.0917199872632	0.0616227850813	0.187344297369	-0.032691121633	-0.00706443281763	0.32038534921	-0.0110151267145	-0.0279918261382	0.447744295751	0.0208346647424	0.320760803396	-3.10231808547	29.9247731432	6.90000991611
16	3.72526079951	-0.391400657154	-1.39716903866	6.75016626353	5.70063233194	8.27311541393	-0.216471366909	0.520593266563	0.439471547421	-0.00619983808183	0.253980128686	0.278400863012	-0.0359358184169	-0.180114012813	-0.00653759042097	0.267799954528	0.00644072572933	-0.0670914760041	0.405458015624	0.0368308479529	0.376676909944	-12.8000355832	30.9190267218	3.45083744921
17	7.69129325942	-0.0967769980564	0.313093226192	4.47313340776	0.184414106417	2.52317200258	0.378312445405	1.20753939188	-0.882898701387	-0.297016574087	-0.515684529838	-0.130808287208	0.695964870823	0.740217802123	0.270063468362	0.516065826126	0.104301415303	-0.0203739855437	0.539656309928	-0.196598703529	0.385629451501	12.521734273	17.3413102396	4.96032835254
18	7.73048774228	2.94814967414	4.68743339748	5.0537461915	4.36700360161	7.03746337966	0.269771333015	-0.43084835817	-0.516870583298	0.428029422478	-0.129265741149	-0.259500826685	0.491654907377	0.195640490521	-0.135645593173	0.455289685497	0.07555017023	-0.0677575926978	0.503802824074	-0.00680259549752	0.427573335749	12.6938498634	17.4452799918	20.0718499767
19	8.49548577202	3.88100545663	4.59117763842	5.70213984898	3.5702264143	6.10140599801	0.286806583114	-0.954393038138	-0.090646581723	0.0235737417966	-0.468224005884	0.251783425971	0.632494115371	-0.74381812009	0.144063226365	0.432074771212	-0.0143231439374	-0.0172806277469	0.517550291626	0.024713052951	0.305888426327	0.621993371734	19.7290712558	17.6761307806
20	1.0594834234	0.103758398443	-0.241046400059	4.25614850167	0.19490962216	2.73864020374	0.195093445337	-0.0594010210809	-0.0743132400258	-0.0522124970156	-0.171465166522	-0.485984070078	0.0583656261948	0.193346589308	-0.0182984858892	0.388483309482	0.0153233481103	-0.0822131056132	0.368588154936	-0.0341207594343	0.421722257427	5.51567992208	30.1125635431	13.6862067398

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 100 through 118 )	C	I	100 - 118	79 - 97
2	2	chain 'C' and (resid 119 through 129 )	C	I	119 - 129	98 - 108
3	3	chain 'C' and (resid 130 through 152 )	C	I	130 - 152	109 - 131
4	4	chain 'D' and (resid 21 through 34 )	D	M	21 - 34	1 - 14
5	5	chain 'D' and (resid 35 through 49 )	D	M	35 - 49	15 - 29
6	6	chain 'D' and (resid 50 through 80 )	D	M	50 - 80	30 - 60
7	7	chain 'D' and (resid 81 through 129 )	D	M	81 - 129	61 - 109
8	8	chain 'D' and (resid 130 through 153 )	D	M	130 - 153	110 - 133
9	9	chain 'A' and (resid 23 through 34 )	A	A	23 - 34	1 - 12
10	10	chain 'A' and (resid 35 through 72 )	A	A	35 - 72	13 - 50
11	11	chain 'A' and (resid 73 through 129 )	A	A	73 - 129	51 - 107
12	12	chain 'A' and (resid 130 through 153 )	A	A	130 - 153	108 - 131
13	13	chain 'B' and (resid 23 through 34 )	B	F	23 - 34	1 - 12
14	14	chain 'B' and (resid 35 through 72 )	B	F	35 - 72	13 - 50
15	15	chain 'B' and (resid 73 through 129 )	B	F	73 - 129	51 - 107
16	16	chain 'B' and (resid 130 through 153 )	B	F	130 - 153	108 - 131
17	17	chain 'C' and (resid 22 through 34 )	C	I	22 - 34	1 - 13
18	18	chain 'C' and (resid 35 through 49 )	C	I	35 - 49	14 - 28
19	19	chain 'C' and (resid 50 through 65 )	C	I	50 - 65	29 - 44
20	20	chain 'C' and (resid 66 through 99 )	C	I	66 - 99	45 - 78

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