PDB-9enw: Apo GES-1 beta-Lactamase

ID or keywords:

Entry

Database: PDB / ID: 9enw

Title

Apo GES-1 beta-Lactamase

Components

beta-lactamase

Keywords

ANTIMICROBIAL PROTEIN / beta-lactamase / antibiotic resistance / enzyme / apo

Function / homology

Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / beta-lactam antibiotic catabolic process / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like / beta-lactamase / beta-lactamase activity / response to antibiotic / Beta-lactamase GES-1

Function and homology information

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.66 Å

Authors

Beer, M. / Hinchliffe, P. / Spencer, J.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Apo GES-1 beta-Lactamase
Authors: Beer, M. / Hinchliffe, P. / Spencer, J.

History

Deposition	Mar 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9enw.cif.gz	377 KB	Display	PDBx/mmCIF format
PDB format	pdb9enw.ent.gz	256 KB	Display	PDB format
PDBx/mmJSON format	9enw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9enw_validation.pdf.gz	448.4 KB	Display	wwPDB validaton report
Full document	9enw_full_validation.pdf.gz	450.6 KB	Display
Data in XML	9enw_validation.xml.gz	30 KB	Display
Data in CIF	9enw_validation.cif.gz	41.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/en/9enw ftp://data.pdbj.org/pub/pdb/validation_reports/en/9enw	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	#164 - Aug 2013 Serotonin Receptor similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2) #29 - May 2002 Penicillin-binding Proteins similarity (1)

Deposited unit

A: beta-lactamase

B: beta-lactamase

hetero molecules

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

1

A: beta-lactamase

hetero molecules

defined by author
Evidence: gel filtration
31.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.630, 80.610, 71.070
Angle α, β, γ (deg.)	90.000, 101.400, 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	beta-lactamase Mass: 31469.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ges-1, blaGES-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJY7, beta-lactamase
#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 1.9 Å³/Da / Density % sol: 35.33 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 20mM HEPES pH 7.6 10% PEG8000, 10% PEG1000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8153 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 12, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8153 Å / Relative weight: 1
Reflection	Resolution: 1.66→52.71 Å / Num. obs: 55622 / % possible obs: 100 % / Redundancy: 6.8 % / B_iso Wilson estimate: 21.06 Å² / CC_1/2: 0.995 / R_pim(I) all: 0.085 / Net I/σ(I): 5.4
Reflection shell	Resolution: 1.66→1.69 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2769 / CC_1/2: 0.249 / R_pim(I) all: 1.151

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.66→41.79 Å / SU ML: 0.3066 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.8724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2511	2741	4.93 %
R_work	0.2022	52820	-
obs	0.2046	55561	99.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.57 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→41.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4007	0	30	490	4527

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0099	4143
X-RAY DIFFRACTION	f_angle_d	1.0505	5608
X-RAY DIFFRACTION	f_chiral_restr	0.0561	637
X-RAY DIFFRACTION	f_plane_restr	0.0099	725
X-RAY DIFFRACTION	f_dihedral_angle_d	14.565	1546

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 (%)
1.66-1.69	0.4208	130	0.3946	2632	X-RAY DIFFRACTION	99.71
1.69-1.72	0.4352	149	0.393	2595	X-RAY DIFFRACTION	99.75
1.72-1.75	0.3915	147	0.3745	2627	X-RAY DIFFRACTION	99.82
1.75-1.79	0.3615	124	0.3448	2632	X-RAY DIFFRACTION	99.93
1.79-1.83	0.391	140	0.3142	2626	X-RAY DIFFRACTION	100
1.83-1.87	0.3201	140	0.2836	2664	X-RAY DIFFRACTION	99.93
1.87-1.92	0.2653	131	0.2758	2628	X-RAY DIFFRACTION	99.86
1.92-1.97	0.3374	136	0.2562	2620	X-RAY DIFFRACTION	99.78
1.97-2.03	0.3053	140	0.2526	2659	X-RAY DIFFRACTION	99.96
2.03-2.09	0.3229	142	0.2449	2602	X-RAY DIFFRACTION	99.78
2.09-2.17	0.2545	135	0.222	2638	X-RAY DIFFRACTION	99.93
2.17-2.25	0.275	143	0.2021	2637	X-RAY DIFFRACTION	99.75
2.25-2.36	0.2853	130	0.199	2637	X-RAY DIFFRACTION	99.96
2.36-2.48	0.2418	136	0.1902	2648	X-RAY DIFFRACTION	99.93
2.48-2.63	0.2438	155	0.1864	2627	X-RAY DIFFRACTION	100
2.64-2.84	0.2656	128	0.1943	2661	X-RAY DIFFRACTION	99.68
2.84-3.12	0.2433	125	0.1847	2647	X-RAY DIFFRACTION	99.96
3.12-3.58	0.2401	142	0.1621	2658	X-RAY DIFFRACTION	99.75
3.58-4.5	0.1755	127	0.1426	2670	X-RAY DIFFRACTION	99.93
4.51-41.79	0.1704	141	0.1648	2712	X-RAY DIFFRACTION	99.86

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	2.75219117168	-0.730313649427	-0.929128950202	1.31882784218	0.554893707257	1.00138109408	-0.00810533138872	0.248850893179	-0.457629330705	-0.175888134117	-0.0860458903986	0.254231175184	0.204716340747	-0.1121759695	0.0613320046887	0.361008460389	0.017996525497	-0.0589775243619	0.212066546949	-0.0346154518734	0.282408926032	6.52755990271	-18.643026415	25.7203435633
2	1.39384930084	0.173671971321	0.317115080147	0.861489115443	-0.0872907850158	0.594280508544	0.178910822834	-0.152442102673	-0.111112284613	0.00754377284291	-0.0867083703414	0.336992042976	0.157390994969	-0.0678145173022	-0.100120392068	0.242642371161	-0.0201152233437	-0.0251235421894	0.162872894015	0.0376246625147	0.263225821595	2.4169646717	-11.7732691477	35.0290204199
3	4.35485056632	-2.69285581615	-1.30354657079	3.23300106011	0.787027708795	1.18882219034	-0.0643215688918	-0.228696114809	-0.0660050777616	0.106464725627	0.141143430387	0.284065660272	0.0236142322606	-0.00873022542118	-0.0538005939474	0.224480742187	-0.00393393897871	-0.00175233854474	0.159343763345	0.0111240956801	0.172742602234	2.03654839734	8.61374739122	35.4154164112
4	1.14022903555	0.451546544092	-0.291395821194	0.867684445285	-0.204034103028	1.52131908261	0.0299329846093	0.0851589747874	-0.0869635000462	0.0584278546864	0.0330834545317	0.157271088215	0.122135172309	-0.0679772414169	-0.0367336167704	0.154916846112	-0.00666468880149	-0.0125109468383	0.11268704705	0.0073906021822	0.162816354349	11.0074552178	19.2781114934	28.639219525
5	0.755396243988	-0.152012176058	0.152484143306	1.1685404671	-0.0980340162914	0.609253306817	-0.0816398831596	0.0278780096471	0.155380317487	0.052881688577	0.00772509792594	-0.0237406137529	-0.241981700259	-0.00824322305052	0.0890386170359	0.235394745698	0.00724864157723	0.0111329127186	0.163465634862	0.00209887126199	0.232525560325	8.0796779606	14.5268953395	30.101484846
6	1.79336323488	0.00195576262833	-0.0763019423354	1.70411880126	0.0579462689059	1.33727992677	-0.13409556384	-0.0816125334944	0.015443241635	0.393622255874	0.0706252652858	-0.173002767387	0.0366827555216	-0.00569748344264	0.0617686601096	0.289624038085	0.0134544860352	-0.0126715557717	0.182592857372	0.0217179715704	0.204356455645	8.2079217942	3.37701217369	41.9141195857
7	1.05715267071	0.105707055618	0.366185239253	0.634610135084	-0.131319960886	0.688786672326	-0.0541241194167	-0.0961735135984	-0.242834903775	0.0414670844552	0.0371057443374	-0.0843304309436	0.0782565225962	-0.0283542478008	0.0132150208624	0.202977564302	-0.0142034916814	-0.00629055967533	0.129775234619	0.0210610492042	0.190706260265	7.71476744359	-3.4283636456	36.430426287
8	0.363893008761	-0.205790500585	-0.518893476421	0.152654878122	0.135918264216	1.3740974472	-0.0454513694965	0.0404656473606	-0.0714275627879	-0.0350334124165	-0.048244557569	0.179769528095	-0.0222309124313	-0.195476231878	0.110321236301	0.174021239159	0.00576855123296	0.0186733012177	0.20347529107	0.00298415139035	0.283870646344	-7.15635096466	7.7682335311	29.2963836392
9	0.970260772185	0.237782289304	-0.211989565282	1.02295183337	0.126502137054	0.333872715107	0.0856973909847	0.200542910832	-0.0584216696933	-0.237800092991	-0.0860997827584	-0.0129210231651	-0.0181584250884	-0.0597579966719	-0.00162639704689	0.228759132368	0.000610582229296	0.0167308212562	0.217750157487	0.019182484733	0.186013511367	0.314902944335	-3.21183190181	17.3954158753
10	0.127183847549	0.125218778374	0.37983458772	1.07015600798	-0.0438112211906	1.30550741362	0.0238291934303	-0.119671340996	0.0504251166618	0.000329993987984	-0.0750184136501	-0.125935107826	0.0456625366097	-0.0740993542926	0.034065366169	0.219824039639	0.00424313078146	-0.0178117281345	0.138078145732	-0.00148858560371	0.207406643554	4.72546547153	-3.25658229764	25.1395923521
11	3.93727860466	-0.671657249553	-0.54357734649	1.4612094263	-0.109894511939	1.67205105575	0.104133403329	0.113364785966	-0.241856460053	-0.0552684491486	-0.0463013029746	0.139761129173	0.210103282038	-0.166798067838	-0.0944945114528	0.233100349966	-0.0231052868584	-0.0223849899581	0.141488776466	-0.00605532638791	0.193301191889	2.70726510447	-9.21499401965	25.5579554626
12	4.01130188235	0.804216337713	-0.490952323517	1.07093683356	-0.29774883175	1.05752121174	0.173256560188	0.262743492591	-0.271266797149	-0.0863881577726	-0.0174767292286	-0.047503412148	0.22799643969	-0.0806927188641	-0.130859817178	0.305330872691	0.0113136422431	-0.0382672675006	0.192963648206	0.00577219264923	0.215441004925	4.2755868169	-12.7969617457	19.2516409783
13	1.68974564585	-0.59243800528	-1.49254844076	0.499588953425	0.777499940529	1.87155059524	0.20862525737	0.0414089179212	0.223530844733	-0.282206825627	0.0439663250787	-0.277196698578	-0.457735803059	0.276895969069	-0.201774555213	0.316388715972	-0.0623416762439	0.0256516050189	0.313934669155	0.0636232478714	0.306204480962	20.1319957907	32.1867790918	-2.95385578199
14	0.866909932677	-0.0558704297924	0.0869022147782	1.0509496717	-0.030760663019	0.76448909623	-0.106896593904	0.154983752624	0.0679773443771	-0.144818172082	0.0520855234325	0.180122036084	-0.0451611538507	-0.058687377483	0.0666109133856	0.198538670314	-0.00727251148663	-0.00212146822609	0.213261299997	0.0232647642887	0.160769287855	-2.54483946915	22.6818746304	6.80753558866
15	0.515656394017	0.317480931865	-0.370135134252	0.681976440771	-0.263078450243	0.418537979769	0.00276718825748	0.0853013683452	0.0621185317417	-0.118921606518	0.0334626493232	0.0882052912051	-0.00457728380619	-0.0582891973202	-0.0301821472853	0.233238128026	-0.00387606775839	-0.0131061444598	0.214158568982	0.0238280812	0.193071720544	1.12222138122	22.4574804136	7.29672108397
16	1.39517755491	-0.520261353631	0.0302325497272	2.17496532856	0.816008291532	1.8573962282	0.0162654299521	0.0251715692437	0.167604176943	-0.0969232302732	0.0671497020498	-0.192445316574	-0.249400374206	-0.0292170157694	-0.0821162464012	0.272812432819	-0.0462493109066	-0.0165997279911	0.231630310726	0.0245176156851	0.200179904164	13.9007614665	28.8440830474	4.23970938439
17	1.60207245702	-0.217109080858	-0.0184314890918	1.99841072406	0.360095936457	1.69307048777	0.119165076884	0.1254653887	-0.0234625904661	0.00611906679069	-0.0478004260655	-0.219393629778	0.0120488235488	0.139266289575	-0.0692049876764	0.213828044145	-0.0301827301129	-0.0179144340906	0.206123800478	0.0208286249489	0.190448870737	21.0235633158	26.5336946191	4.5731314897

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 23 through 45 )	A	A	23 - 45	1 - 23
2	2	chain 'A' and (resid 46 through 62 )	A	A	46 - 62	24 - 40
3	3	chain 'A' and (resid 63 through 80 )	A	A	63 - 80	41 - 58
4	4	chain 'A' and (resid 81 through 110 )	A	A	81 - 110	59 - 88
5	5	chain 'A' and (resid 111 through 137 )	A	A	111 - 137	89 - 115
6	6	chain 'A' and (resid 138 through 162 )	A	A	138 - 162	116 - 140
7	7	chain 'A' and (resid 163 through 190 )	A	A	163 - 190	141 - 168
8	8	chain 'A' and (resid 191 through 207 )	A	A	191 - 207	169 - 185
9	9	chain 'A' and (resid 208 through 224 )	A	A	208 - 224	186 - 202
10	10	chain 'A' and (resid 225 through 246 )	A	A	225 - 246	203 - 224
11	11	chain 'A' and (resid 247 through 263 )	A	A	247 - 263	225 - 241
12	12	chain 'A' and (resid 264 through 284 )	A	A	264 - 284	242 - 262
13	13	chain 'B' and (resid 21 through 45 )	B	C	21 - 45	1 - 25
14	14	chain 'B' and (resid 46 through 100 )	B	C	46 - 100	26 - 80
15	15	chain 'B' and (resid 101 through 246 )	B	C	101 - 246	81 - 226
16	16	chain 'B' and (resid 247 through 263 )	B	C	247 - 263	227 - 243
17	17	chain 'B' and (resid 264 through 284 )	B	C	264 - 284	244 - 264

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