PDB-9s5k: ADC-30 class C beta-lactamase in a di-covalent complex with benzo...

ID or keywords:

Entry

Database: PDB / ID: 9s5k

Title

ADC-30 class C beta-lactamase in a di-covalent complex with benzoxaborole AK-431

Components

Beta-lactamase

Keywords

ANTIMICROBIAL PROTEIN / complex / boronate / di-covalent / antibiotic resistance

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.38 Å

Authors

Hinchliffe, P. / Spencer, J.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: ADC-30 class C beta-lactamase in a di-covalent complex with benzoxaborole AK-431
Authors: Hinchliffe, P. / Spencer, J.

History

Deposition	Jul 29, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9s5k.cif.gz	388.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9s5k.ent.gz		Display	PDB format
PDBx/mmJSON format	9s5k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9s5k_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9s5k_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9s5k_validation.xml.gz	33.8 KB	Display
Data in CIF	9s5k_validation.cif.gz	49.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/9s5k ftp://data.pdbj.org/pub/pdb/validation_reports/s5/9s5k	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	#29 - May 2002 Penicillin-binding Proteins similarity (2) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

B: Beta-lactamase

A: Beta-lactamase

hetero molecules

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

1

B: Beta-lactamase

hetero molecules

defined by author
Evidence: gel filtration, none
41 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.381, 83.545, 208.316
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	Beta-lactamase Mass: 40569.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ampC, adc30, FPK63_09015, FPK87_18695, FQZ18_06125 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: A7XM81, beta-lactamase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-A1JLW / 2-[(9~{R})-8-oxa-7-boranidabicyclo[4.3.0]nona-1,3,5-trien-9-yl]ethanoic acid Mass: 174.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₈BO₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 958 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.33 Å³/Da / Density % sol: 47.13 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: ADC-30 (5 mg/mL) in 24% w/v polyethylene glycol (PEG) 2000, 0.1 M succinate/ phosphate/ glycine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 9, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95374 Å / Relative weight: 1
Reflection	Resolution: 1.38→52.08 Å / Num. obs: 155254 / % possible obs: 99.1 % / Redundancy: 13.1 % / B_iso Wilson estimate: 17.58 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.034 / Net I/σ(I): 10
Reflection shell	Resolution: 1.38→1.4 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7524 / CC_1/2: 0.494 / R_pim(I) all: 0.423

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.38→52.08 Å / SU ML: 0.1472 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1853	7565	4.88 %
R_work	0.1649	147502	-
obs	0.1659	155067	99.03 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 23.65 Å²

Refinement step

Cycle: LAST / Resolution: 1.38→52.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5698	0	46	958	6702

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0053	6033
X-RAY DIFFRACTION	f_angle_d	0.8097	8202
X-RAY DIFFRACTION	f_chiral_restr	0.0821	888
X-RAY DIFFRACTION	f_plane_restr	0.0064	1068
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8083	2289

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 (%)
1.38-1.4	0.2777	240	0.2811	4791	X-RAY DIFFRACTION	96.69
1.4-1.41	0.2742	240	0.2583	4819	X-RAY DIFFRACTION	98.69
1.41-1.43	0.2865	200	0.2475	4836	X-RAY DIFFRACTION	97.88
1.43-1.45	0.2437	268	0.2282	4801	X-RAY DIFFRACTION	96.77
1.45-1.47	0.2463	267	0.2156	4817	X-RAY DIFFRACTION	99.82
1.47-1.49	0.2374	239	0.219	4823	X-RAY DIFFRACTION	97.51
1.49-1.51	0.2387	242	0.2001	4777	X-RAY DIFFRACTION	98.24
1.51-1.53	0.2154	241	0.2029	4876	X-RAY DIFFRACTION	99.57
1.53-1.55	0.2333	244	0.1966	4821	X-RAY DIFFRACTION	96.94
1.55-1.58	0.2245	231	0.207	4914	X-RAY DIFFRACTION	99.96
1.58-1.61	0.2169	255	0.2014	4831	X-RAY DIFFRACTION	97.23
1.61-1.64	0.1969	233	0.2011	4858	X-RAY DIFFRACTION	99.96
1.64-1.67	0.2057	270	0.1879	4871	X-RAY DIFFRACTION	98.04
1.67-1.7	0.2147	255	0.1853	4880	X-RAY DIFFRACTION	99.81
1.7-1.74	0.2121	251	0.1838	4879	X-RAY DIFFRACTION	98.35
1.74-1.78	0.2077	259	0.1722	4901	X-RAY DIFFRACTION	100
1.78-1.82	0.1965	259	0.172	4869	X-RAY DIFFRACTION	98.73
1.82-1.87	0.2116	284	0.1728	4906	X-RAY DIFFRACTION	99.96
1.87-1.93	0.2124	237	0.1753	4913	X-RAY DIFFRACTION	99.04
1.93-1.99	0.1991	229	0.1799	4943	X-RAY DIFFRACTION	99.27
1.99-2.06	0.1998	252	0.1639	4965	X-RAY DIFFRACTION	99.81
2.06-2.14	0.1785	276	0.1543	4927	X-RAY DIFFRACTION	99.66
2.14-2.24	0.1793	266	0.155	4936	X-RAY DIFFRACTION	99.66
2.24-2.36	0.2131	245	0.1611	4991	X-RAY DIFFRACTION	99.79
2.36-2.51	0.195	261	0.1638	4988	X-RAY DIFFRACTION	99.87
2.51-2.7	0.1961	256	0.169	5030	X-RAY DIFFRACTION	99.92
2.7-2.97	0.1844	250	0.1621	5015	X-RAY DIFFRACTION	99.96
2.97-3.4	0.1721	285	0.1548	5025	X-RAY DIFFRACTION	100
3.4-4.29	0.1484	268	0.139	5146	X-RAY DIFFRACTION	100
4.29-52.08	0.1398	262	0.1399	5353	X-RAY DIFFRACTION	99.82

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	2.96940418319	0.227121812576	-0.120902737683	1.73929235913	0.036765081678	1.04105601834	-0.0223441973748	-0.170036773207	0.15141452086	0.29443280923	0.0522091050838	0.151317152839	-0.140573929534	-0.0818475464021	-0.0458314878312	0.228227349911	0.00599679292883	0.0224961637621	0.101078128903	0.0124728947099	0.147356623303	-20.3661782652	27.6734273528	56.438187414
2	0.805504176112	-0.115728583515	-0.21343636231	1.82505803875	0.400825146292	0.986593585036	-0.0200335941232	0.0711172013845	0.0674943161007	-0.0732767983913	0.00586427671607	0.142403428988	-0.0749474844584	-0.0695771078845	0.0169529178128	0.113036309029	-0.00390944199819	0.00299343083628	0.107810954687	0.0176252415653	0.109199370945	-18.9762344445	22.3456987296	41.2003458798
3	4.28642739282	0.465797695665	-0.627581148717	1.76157624089	0.172891171957	2.67655439228	-0.135059522327	0.318016516107	-0.314508797254	-0.274942302687	-0.0218596608506	-0.0451858002184	0.40968759721	0.0627444093498	0.158536413112	0.327808949134	0.0202831652555	0.0501811715904	0.179949889001	-0.0621323418968	0.203126670709	-8.59920068862	-4.55994924186	26.7141495795
4	3.73948276554	0.981416817041	-1.14078973562	2.79884578698	-0.169121568163	3.23486725633	-0.0463500023386	0.169571993575	0.00689357844803	-0.234759080802	-0.0273712607223	-0.257959946247	0.0319295775175	0.311684206772	0.100969465714	0.157467687957	0.0289745597161	0.0296157540517	0.179867348906	0.00472941420108	0.148219400401	0.386413461091	5.190593219	32.3715481701
5	1.06896458364	0.315255852964	-0.309907300541	1.394176668	0.313454461847	3.14871973362	-0.00434254488903	-0.017129617382	-0.142444740247	-0.0602270626246	-0.010325990522	-0.207869469991	0.350326186998	0.326467957639	0.00948961753374	0.177670997656	0.0309984098037	0.0420319586091	0.137432284404	-0.00297834015209	0.167585618356	-4.06838892721	0.243565406389	35.5819810188
6	1.71270580919	1.90789372431	0.946964354047	3.97174083248	1.5848072004	1.37492668291	0.0167886637936	0.090917122227	0.0868796744575	-0.160845561889	-0.0269699029475	0.14862225157	-0.0278336820406	-0.00287134697489	0.0167115845069	0.170209063433	0.000848245039261	0.0170457250093	0.158125512167	0.0303299543138	0.1166006685	-15.2073938101	21.9941264886	31.8389852783
7	0.702233061328	0.526766453845	0.0768760888918	2.24128718847	0.0510214891189	0.491308427889	0.0451621066397	0.0670392745036	0.0371116273136	-0.0924208239723	-0.00514909975501	-0.0264848784268	-0.0763162050734	0.0392813708098	-0.0444911690677	0.134971259968	-0.00898731938864	-0.00158262988897	0.113020733998	0.00191805927881	0.100436990741	-15.5096316495	18.3963841117	37.9069286649
8	5.94905513445	-1.66170413778	0.877919470567	5.72632312113	-2.59421511899	7.05800734134	0.0166225870486	0.251679527982	0.00383398262909	-0.179080542786	-0.311631362209	0.523225943518	0.360874042083	-0.760299474381	0.271586289272	0.125815288631	-0.0301803265217	-0.000726396620117	0.212170830392	-0.0707155844116	0.219595708451	-28.5422084245	4.75066299086	37.5951971835
9	0.313561626142	-0.207919506111	-0.0779860740629	2.14330802353	-0.254389336213	0.806328313648	-0.0365126158252	0.00210991641077	-0.0515770046401	0.0559371519622	0.0280581494775	-0.000208811852025	0.0755681130318	0.022875211332	0.0117733532198	0.131447539768	-0.0024799453731	0.0145831832796	0.105519613287	-0.00451932160057	0.127820827071	-13.5722414966	5.66256282448	50.9442629775
10	3.82713016228	0.972851983374	-1.26891470396	3.5644329252	-1.69117751556	3.03059976964	-0.0808089189443	-0.139485248544	-0.165864665424	0.217403111058	-0.0201649375771	-0.0235806792031	-0.0667630764807	0.0494202885548	0.118649406119	0.132742883081	0.00800495179276	0.0115923794951	0.0495817669303	-0.0222400722844	0.098051739588	-16.4674206797	19.2491972476	54.1258350832
11	1.6941779095	-0.172492633935	-0.301779219864	1.73131384836	0.719176637092	2.03454377928	-0.028939433199	-0.153336146701	-0.309654216341	0.191922809402	0.0457416885934	-0.0941635929075	0.464292000071	0.206861205889	-0.02101016664	0.229378810248	0.0611271885368	-0.00517202621657	0.133694240347	0.00496717682076	0.192861120729	-0.522088906361	-7.26785529077	78.2195908616
12	2.15027822297	-0.329974325396	-0.24146878086	1.361230031	0.272756999942	1.30102170338	0.0579768739705	-0.119607838631	0.230225906292	-0.131345821672	-0.0213738168032	0.0304079660897	-0.234294602849	-0.0339550099202	-0.0325890631966	0.164789561267	0.00891940421537	0.00586718374824	0.157014291064	-0.0222276520115	0.113019853945	-15.7592482572	22.3245914657	90.4749986599
13	1.03949504852	0.0510113843786	0.352339132587	0.726700436831	0.543278192241	2.32709061446	0.0306940257232	-0.0871109575856	0.0108706783186	-0.0485082023451	0.0179799148505	-0.0860130433803	-0.0512172575943	0.1759866924	-0.0522768604642	0.139342566305	0.0111170314756	0.0230057374775	0.160525586862	-0.00241508755316	0.133863535124	-1.22029861017	10.7770545047	82.1919379038
14	2.16863720284	-0.677218954039	-0.612705620089	3.40997222519	0.471020282365	1.10716545947	-0.0693115055224	-0.49443700385	-0.104781336375	0.275416470825	-0.0201046044148	0.0545197364734	0.229349362252	-0.0456228072173	0.0813485964582	0.169051348216	-0.00843306994691	0.0210972370774	0.261326141944	0.0258033468958	0.119815576203	-17.1530616117	3.31733232677	97.9964446173
15	3.4721743295	-0.805589472374	1.74378004977	2.72482434265	-1.33552007242	7.40541983209	0.0502683158635	-0.343187659765	-0.218426434209	0.194548273857	0.00702930298639	-0.0312912961683	0.259205085448	0.0043221025165	-0.0796069005102	0.136087459955	-0.00200282598607	0.00974694511986	0.121593982117	0.0156321428697	0.11679726333	-7.93318565489	0.374313513995	89.6890670829
16	3.41036304014	0.359764953482	-0.00553958706477	3.07927859926	-0.288526871375	2.91022334939	0.00991721826958	-0.378345122055	-0.381325128985	0.335602997976	-0.0159772863692	-0.0150734838101	0.497154894632	0.00825605041835	-0.0442124094442	0.238007245381	0.0270082948531	0.00207901472207	0.120925664343	0.0295226129885	0.161765664465	-7.60515962376	-6.93411544566	86.6662922716
17	2.00006397435	1.99997632521	2.00001265236	2.00003489569	1.99997088053	1.99999928734	-5.00633567351	-9.20410441097	4.56989587678	7.44051221464	4.92313762845	-1.06849433759	-1.14883355087	6.26583676614	0.100756777301	0.673954509745	0.475721126628	-0.231685264287	0.775774001941	-0.180413969375	0.711122926972	-25.0284205946	35.4434836327	40.3238608321

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 'B' and (resid 1 through 34 )	B	A	1 - 34	1 - 34
2	2	chain 'B' and (resid 35 through 79 )	B	A	35 - 79	35 - 79
3	3	chain 'B' and (resid 80 through 105 )	B	A	80 - 105	80 - 105
4	4	chain 'B' and (resid 106 through 136 )	B	A	106 - 136	106 - 136
5	5	chain 'B' and (resid 137 through 166 )	B	A	137 - 166	137 - 166
6	6	chain 'B' and (resid 167 through 208 )	B	A	167 - 208	167 - 208
7	7	chain 'B' and (resid 209 through 239 )	B	A	209 - 239	209 - 239
8	8	chain 'B' and (resid 240 through 256 )	B	A	240 - 256	240 - 256
9	9	chain 'B' and (resid 257 through 329 )	B	A	257 - 329	257 - 329
10	10	chain 'B' and (resid 330 through 359 )	B	A	330 - 359	330 - 359
11	11	chain 'A' and (resid 2 through 62 )	A	D	2 - 62	1 - 61
12	12	chain 'A' and (resid 63 through 166 )	A	D	63 - 166	62 - 165
13	13	chain 'A' and (resid 167 through 256 )	A	D	167 - 256	166 - 255
14	14	chain 'A' and (resid 257 through 307 )	A	D	257 - 307	256 - 306
15	15	chain 'A' and (resid 308 through 329 )	A	D	308 - 329	307 - 328
16	16	chain 'A' and (resid 330 through 359 )	A	D	330 - 359	329 - 358
17	17	chain 'D' and (resid 1 through 1 )	D	H	1	1

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Assembly

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Experiment

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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