PDB-8zxs: Crystal structure of multidrug efflux transporter OqxB from Klebs...

ID or keywords:

Entry

Database: PDB / ID: 8zxs

Title

Crystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae

Components

Efflux pump membrane transporter

Keywords

MEMBRANE PROTEIN / Multidrug efflux transporter / Membrane transporter / Antimicrobial resistance / AMR / Klebsiella pneumoniae / TRANSPORT PROTEIN

Function / homology

Hydrophobe/amphiphile efflux-1 HAE1 / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / Acriflavin resistance protein / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter

Function and homology information

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Murakami, S. / Yamashita, E. / Okada, U.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	JP21H02412	Japan
Japan Society for the Promotion of Science (JSPS)	JP18K06079	Japan
Japan Society for the Promotion of Science (JSPS)	21K19337	Japan

Citation

Journal: To Be Published
Title: Crystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae
Authors: Murakami, S. / Yamashita, E. / Okada, U.

History

Deposition	Jun 15, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 18, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zxs.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb8zxs.ent.gz	1015.1 KB	Display	PDB format
PDBx/mmJSON format	8zxs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8zxs_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8zxs_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8zxs_validation.xml.gz	130 KB	Display
Data in CIF	8zxs_validation.cif.gz	161.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/8zxs ftp://data.pdbj.org/pub/pdb/validation_reports/zx/8zxs	HTTPS FTP

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Related structure data

Related structure data	7cz9
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	#95 - Nov 2007 Multidrug Resistance Transporters similarity (4)

Deposited unit

A: Efflux pump membrane transporter

B: Efflux pump membrane transporter

C: Efflux pump membrane transporter

hetero molecules

346 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	121.392, 165.939, 249.032
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

#1: Protein	Efflux pump membrane transporter Mass: 114393.211 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: The 6-His residues are purification tag. / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: bepE_2, bepE_1, B5L96_27435, GJJ13_005705, GJJ18_08150, NCTC204_03625, NCTC9637_01899, QIG75_20820, SAMEA4364603_03846 Production host: Escherichia coli (E. coli) / References: UniProt: U5U6L7
#2: Sugar	ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: 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
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 3.65 Å³/Da / Density % sol: 66.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 10% PEG 4000, 0.1M ADA, 0.2M magnesium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.75→49.34 Å / Num. obs: 130594 / % possible obs: 99.65 % / Redundancy: 7.33 % / B_iso Wilson estimate: 93.76 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.082 / R_pim(I) all: 0.032 / Net I/av σ(I): 12.9 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.75→2.8 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 44929 / CC_1/2: 0.498 / % possible all: 95.19

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
Coot		model building
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→43.04 Å / SU ML: 0.4744 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.619
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2877	6532	5.01 %
R_work	0.2363	123910	-
obs	0.2389	130442	99.6 %

Solvent computation

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

Displacement parameters

B_iso mean: 124.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→43.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23767	0	216	1	23984

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	24459
X-RAY DIFFRACTION	f_angle_d	0.8882	33290
X-RAY DIFFRACTION	f_chiral_restr	0.0506	3975
X-RAY DIFFRACTION	f_plane_restr	0.0064	4250
X-RAY DIFFRACTION	f_dihedral_angle_d	9.3034	3421

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 (%)
2.75-2.78	0.4218	204	0.4081	3854	X-RAY DIFFRACTION	94.44
2.78-2.81	0.4266	214	0.3986	4141	X-RAY DIFFRACTION	99.77
2.81-2.85	0.393	178	0.3762	4095	X-RAY DIFFRACTION	99.67
2.85-2.88	0.4162	237	0.3786	4073	X-RAY DIFFRACTION	99.65
2.88-2.92	0.4399	211	0.3972	4102	X-RAY DIFFRACTION	99.77
2.92-2.96	0.4365	239	0.3802	4133	X-RAY DIFFRACTION	99.66
2.96-3	0.3792	216	0.3476	4011	X-RAY DIFFRACTION	99.55
3-3.05	0.3963	224	0.3185	4094	X-RAY DIFFRACTION	99.54
3.05-3.1	0.3587	212	0.2981	4073	X-RAY DIFFRACTION	99.58
3.1-3.15	0.3373	211	0.2825	4123	X-RAY DIFFRACTION	99.75
3.15-3.2	0.3385	228	0.2843	4108	X-RAY DIFFRACTION	99.75
3.2-3.26	0.3029	211	0.2692	4111	X-RAY DIFFRACTION	99.84
3.26-3.32	0.3352	209	0.2685	4094	X-RAY DIFFRACTION	99.63
3.32-3.39	0.3298	213	0.2636	4121	X-RAY DIFFRACTION	99.86
3.39-3.46	0.3234	200	0.2632	4145	X-RAY DIFFRACTION	99.93
3.46-3.55	0.3391	233	0.2602	4126	X-RAY DIFFRACTION	99.93
3.55-3.63	0.3128	220	0.2624	4095	X-RAY DIFFRACTION	99.93
3.63-3.73	0.2986	225	0.2456	4103	X-RAY DIFFRACTION	99.93
3.73-3.84	0.3046	205	0.2408	4157	X-RAY DIFFRACTION	99.91
3.84-3.97	0.2895	235	0.2329	4122	X-RAY DIFFRACTION	99.89
3.97-4.11	0.3001	202	0.2361	4139	X-RAY DIFFRACTION	99.75
4.11-4.27	0.2749	201	0.2256	4171	X-RAY DIFFRACTION	99.98
4.27-4.47	0.2574	224	0.2012	4167	X-RAY DIFFRACTION	99.93
4.47-4.7	0.2423	222	0.1979	4163	X-RAY DIFFRACTION	99.91
4.7-4.99	0.2433	205	0.1941	4164	X-RAY DIFFRACTION	100
5-5.38	0.288	220	0.2154	4178	X-RAY DIFFRACTION	99.98
5.38-5.92	0.2652	251	0.237	4177	X-RAY DIFFRACTION	99.98
5.92-6.77	0.2874	225	0.2406	4230	X-RAY DIFFRACTION	99.96
6.77-8.52	0.2428	216	0.1958	4257	X-RAY DIFFRACTION	99.58
8.52-43.04	0.2708	241	0.2245	4383	X-RAY DIFFRACTION	98.97

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	0.639575428241	0.128807744494	0.119467197615	0.541592662844	0.237243015545	0.818263737553	-0.106663929338	-0.125933737478	-0.138491323952	0.298191554263	0.0451570063841	-0.0547487776314	0.450587604476	-0.0657560658407	-5.87908983635E-5	0.82380756872	0.0358539872769	0.166308212406	0.771492768906	0.0312166042375	0.848566149338	-1.39904292126	-2.09509218996	-12.3515843074
2	0.7051715213	-0.0717178326854	0.0143402284724	-0.0232081381111	-0.305092551849	1.16906236648	0.111246134229	0.066717559154	-0.00472339208711	0.00878721784486	-0.0469443728668	-0.0230487151126	0.411651105284	-0.528288007648	-0.00185733553759	0.725396961609	-0.254469452272	0.0487627825862	0.946405871456	-0.24524062223	0.812030923638	-14.4054059027	-13.122491993	-41.571162953
3	1.11038114118	-0.659427556529	-0.766745684519	1.47465073564	0.455483333625	0.973253450319	-0.0701369091749	-0.214903431175	0.0239853841108	0.0960824845429	-0.175158568752	0.184895294108	0.0211184695308	-0.665191061644	-0.0017909571845	0.601294035395	0.0319096872987	0.00987157027154	0.991807567626	-0.013989498721	0.709216636059	-12.7351045604	20.5897888084	-7.55551067071
4	0.848114725186	-0.380226105763	0.160595731242	0.961844577553	-0.88888762863	0.833525418595	0.0284539744194	0.106830031793	-0.0133162377396	-0.346754374824	-0.274024714273	0.159923076925	0.592941354932	-0.487101173885	-0.00144807849898	0.907498559368	0.287522847045	0.00610452328815	1.50025525694	-0.0903154719692	0.974114143632	-9.69320879837	24.2092975919	-24.455981561
5	0.500181851146	-0.258949800908	0.60635948634	1.14019054973	-0.683138093019	0.803019998772	-0.264056826603	0.551147336607	-0.356096840256	-0.0933945852283	0.36521315471	0.347384514077	0.486238654452	-0.684321032194	-1.45113724533E-6	0.831925526491	-0.150117152543	0.0990823009187	1.19537901175	-0.297547357946	1.04567127669	-12.1199071951	-13.1769123241	-57.3320488324
6	1.99011685521	-0.271060340868	0.0630426682531	0.357286287412	-0.103169846575	1.4828250989	0.149187764581	-0.367443042283	-0.149198703619	0.308840673364	0.0594337535077	0.0766576661282	0.497231203932	-0.311854898731	0.0334707821095	0.928766769559	0.076043310017	-0.154378485505	0.474078242762	0.138904584552	0.683970404419	26.8673196182	-5.49105305325	-9.67386530346
7	0.812828539445	-0.671907544845	0.237278961969	1.12052429984	-0.459556977049	0.235039133654	-0.0995300182853	-0.280267885817	0.0610114052794	0.00702807363063	0.1038992206	-0.38679462988	0.191793134471	0.514881214911	-7.6047931028E-5	1.01460737134	0.0988785546666	-0.0737481643203	1.26374385426	0.0181687974334	0.9020896587	36.1600018037	23.0566371825	8.17187015507
8	1.04520437546	-0.345027356722	-0.825386654093	0.0798819407846	0.239971855757	0.738546809451	0.475494061877	0.438949269591	-0.534056932222	-0.357679471049	-0.064519404815	-0.346466563053	0.433643024383	0.879495063029	-0.0506947777159	1.68086865005	0.599270232877	-0.267664093304	1.19208122417	-0.0489211489504	1.11371818032	45.035472127	-14.7665346944	-10.544942542
9	0.353636227216	0.0814105400206	-0.0613979233278	0.0181024840909	0.0980680273405	0.193632411039	0.166145598778	0.31665047161	-0.400025606656	-0.356981126124	0.0380139629729	0.102490605431	0.299260863235	0.515965623167	0.112241655687	1.95772050201	0.565505074663	-0.132416804793	0.955595363229	-0.3032093338	1.20165959133	35.5443071548	-39.4027915138	-36.5758688429
10	1.72512882863	-1.51125999642	-1.03502735358	1.70675346439	0.591806317788	0.961010834054	-0.198593913635	-1.40137716072	0.859889624819	0.787565053602	0.601244177382	-0.46022897967	0.318687127373	0.430847391383	1.98560581539	1.47925763566	0.470903754726	-0.207757963746	0.741761809774	0.577519583726	0.425991251905	30.448836357	-26.870352566	1.54403985003
11	0.0216609618941	0.110317122433	0.136885011897	0.493971145697	0.635465974976	0.793628554052	0.288629662319	0.614198192671	-0.693168050483	-0.0934262018127	-0.719895366508	0.143009823111	0.561877262815	-0.108939160931	-0.0249819080068	1.68417872175	0.516183532244	-0.215486143093	1.26757429704	0.176012834248	1.15552680259	37.6032958529	-23.9731939933	6.25873571574
12	0.124429873545	0.090670578294	-0.524943663418	0.549110069326	-0.56335818247	2.09727508787	-0.085141168141	-0.020291798368	-0.195020433657	0.0983835817235	0.183681961073	0.0950065116357	0.792585609795	-0.295516911429	-0.00275293065306	1.38558411387	-0.0235251693046	-0.056633429185	1.26750740917	0.134539160223	1.0400873553	20.7579494147	2.9740777873	20.8094518234
13	0.207801334231	0.281029360745	0.439928147776	0.358299420985	0.574121094377	0.581141693958	0.744039582048	-0.338375559805	-0.156010195382	0.567864631605	-0.585141859038	-0.314586494545	0.703203052055	-0.808794768797	-0.027741043884	1.60155477104	-0.168590747375	-0.123613442277	0.907755392013	0.0895944199365	0.738896952203	12.1972777013	-24.7733299905	-4.3902403702
14	1.39945808382	0.597054817112	-0.282506707958	0.243444132894	-0.0489360781057	0.419289015715	0.418068894458	-0.179528198657	-1.07639537443	-0.1196383451	-0.373788532121	-0.0181890055756	-0.264994419588	-0.308464099658	0.0256846715114	2.61391396374	0.304128663724	-0.289259921172	0.929022873971	-0.293290199322	1.75199395237	25.0138069172	-47.5378954603	-27.7766241129
15	0.569441629543	0.402361585916	-0.168462457129	0.404541082474	0.126225575062	1.13694736571	0.328012964682	-0.11825775625	-0.103661720791	0.719910995819	-0.110256376086	-0.206960354317	0.69281318816	0.203461848741	-0.00588103042386	0.638994892295	0.0570351287794	0.0501165501137	0.738830405469	-0.122463287724	0.772874391019	26.1556893458	6.66872894595	-33.5725718307
16	0.199599191615	-0.0620907432078	0.07769254955	0.299165755473	0.16686014624	0.255531482343	0.0400239154812	-0.11698221502	-0.207528630754	0.217940113276	0.139116716344	-0.0372278245976	-0.372816952377	-0.606804738032	-0.00141406726156	0.919301175997	0.0990703848436	0.109863617412	1.12974402825	-0.110040877479	0.860263965447	21.1843786172	23.7185496573	-20.4479290754
17	0.125740095838	-0.112902880272	-0.135355668964	0.119819317064	0.0146353481201	0.222215349534	-0.1171363125	-0.0675460437054	0.171467837621	0.0742454609887	-0.169269616094	0.0125197111269	-0.0897425969463	0.0256930141275	-0.000138459511909	0.680244066627	0.0231391910861	0.01266492978	1.04128540875	-0.133336938139	0.821503864217	7.0685499753	34.918144431	-6.47421516438
18	0.192223311357	0.142685969966	-0.396204949988	0.276192604602	-0.119964175754	0.560705107078	-0.00725768443255	0.731601566197	0.130934073508	-0.244035577328	-0.112022423159	-0.0722247904694	0.0687520410343	-0.337280629863	3.91444848978E-5	0.720259114464	-0.0122057844152	0.00319680492564	1.15500403389	-0.175256670152	1.05622693208	15.8833521476	37.6700386465	-23.7231142084
19	0.770967249705	0.0301090636737	0.228010309728	0.274122747761	-0.0035900821612	1.83366140129	0.0577434525515	0.330769592088	-0.0773631294113	-0.0867943142462	-0.0122471061168	-0.0962628183281	0.246042613019	0.627280116895	0.000472428715934	0.96221318659	0.125013439289	0.0304877490749	1.23246955843	-0.132532426983	0.834374438901	31.8952888409	5.61956016082	-59.7973242798
20	0.54954868788	0.196549294645	0.411284536317	1.19304002885	0.554652268316	0.620489601346	-0.174354794368	0.0589665991064	0.100203319685	-0.140620286518	0.0846729066756	0.0321127159437	0.0414558488684	0.531504623363	-5.28311109293E-5	0.771784637899	-0.0869373868298	-0.0342850427366	1.16258732058	-0.00591167661249	0.934619026568	37.2754462241	33.2711849061	-16.8934248153
21	0.482123634074	0.424907293165	0.459266152781	0.521877904175	0.62935578744	2.6376064794	-0.0844381410787	-0.13299429084	0.399612541552	-0.0311349069587	0.416364278497	-0.51910865102	-0.286882914781	1.96314541212	-0.609847836254	0.500997044156	0.290984956483	0.0376359304459	1.82526494048	-0.232104343453	0.760690621176	47.9085811968	6.20102192883	-38.456648953
22	0.537212259387	-0.0589490611264	0.0555359910785	0.00349787391722	-0.0256968837082	0.838971899864	0.058938917149	0.237041322243	0.127362555467	0.064838964358	0.246603963357	-0.414439457876	0.125883585814	1.01008427823	-0.082271700289	0.727781249135	0.243059212998	0.0325708385864	1.73075023725	-0.437819651881	0.778674129476	43.5952222313	-5.5439400864	-63.7369016777

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 1 through 426 )	A	A	1 - 426	1 - 426
2	2	chain 'A' and (resid 427 through 631 )	A	A	427 - 631	427 - 631
3	3	chain 'A' and (resid 632 through 801 )	A	A	632 - 801	632 - 801
4	4	chain 'A' and (resid 802 through 877 )	A	A	802 - 877	802 - 877
5	5	chain 'A' and (resid 878 through 1040 )	A	A	878 - 1040	878 - 1040
6	6	chain 'B' and (resid 1 through 163 )	B	B	1 - 163	1 - 163
7	7	chain 'B' and (resid 164 through 275 )	B	B	164 - 275	164 - 275
8	8	chain 'B' and (resid 276 through 361 )	B	B	276 - 361	276 - 361
9	9	chain 'B' and (resid 362 through 542 )	B	B	362 - 542	362 - 542
10	10	chain 'B' and (resid 543 through 631 )	B	B	543 - 631	543 - 631
11	11	chain 'B' and (resid 632 through 684 )	B	B	632 - 684	632 - 684
12	12	chain 'B' and (resid 685 through 816 )	B	B	685 - 816	685 - 816
13	13	chain 'B' and (resid 817 through 898 )	B	B	817 - 898	817 - 898
14	14	chain 'B' and (resid 899 through 1042 )	B	B	899 - 1042	899 - 1042
15	15	chain 'C' and (resid 1 through 101 )	C	C	1 - 101	1 - 101
16	16	chain 'C' and (resid 102 through 163 )	C	C	102 - 163	102 - 163
17	17	chain 'C' and (resid 164 through 250 )	C	C	164 - 250	164 - 250
18	18	chain 'C' and (resid 251 through 331 )	C	C	251 - 331	251 - 331
19	19	chain 'C' and (resid 332 through 631 )	C	C	332 - 631	332 - 631
20	20	chain 'C' and (resid 632 through 833 )	C	C	632 - 833	632 - 833
21	21	chain 'C' and (resid 834 through 898 )	C	C	834 - 898	834 - 898
22	22	chain 'C' and (resid 899 through 1041 )	C	C	899 - 1041	899 - 1041

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