PDB-8ttp: Crystal structure of class C beta-lactamase from Escherichia coli...

ID or keywords:

Entry

Database: PDB / ID: 8ttp

Title

Crystal structure of class C beta-lactamase from Escherichia coli in complex with avibactam

Components

Beta-lactamase

Keywords

HYDROLASE / class C bete-lactamase / Escherichia coli / avibactam / Center for Structural Biology of Infectious Diseases / Structural Genomics / CSBID

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

Escherichia coli A35218R (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.43 Å

Authors

Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

1items

Citation

Journal: to be published
Title: Crystal structure of class C beta-lactamase from Escherichia coli in complex with avibactam
Authors: Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A.

History

Deposition	Aug 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 6, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ttp.cif.gz	385.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ttp.ent.gz	258.9 KB	Display	PDB format
PDBx/mmJSON format	8ttp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ttp_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8ttp_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8ttp_validation.xml.gz	36.9 KB	Display
Data in CIF	8ttp_validation.cif.gz	57.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tt/8ttp ftp://data.pdbj.org/pub/pdb/validation_reports/tt/8ttp	HTTPS FTP

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Related structure data

Related structure data	6whf
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSBID-IDP97257

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#29 - May 2002 Penicillin-binding Proteins similarity (3) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	155.614, 46.457, 109.126
Angle α, β, γ (deg.)	90.000, 116.580, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y

Components on special symmetry positions

ID	Model	Components
1	1	B-799- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase Mass: 39859.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli A35218R (bacteria) / Gene: bla(ampc-EC31) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q104Z6

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Non-polymers , 5 types, 903 molecules

#2: Chemical	ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₃N₃O₆S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 887 / 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: 2.21 Å³/Da / Density % sol: 44.41 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH7.5, 10% 2-Propanol, 20% Polyethylene glycol 4K

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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: 0.979 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2019

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.43→50 Å / Num. obs: 127325 / % possible obs: 98.6 % / Redundancy: 4.7 % / B_iso Wilson estimate: 14.07 Å² / R_merge(I) obs: 0.059 / R_pim(I) all: 0.03 / R_rim(I) all: 0.067 / Χ²: 0.937 / Net I/σ(I): 9.7 / Num. measured all: 593927

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.43-1.45	3.1	0.736	5658	0.62	0.455	0.87	0.768	88.1
1.45-1.48	3.6	0.662	6022	0.693	0.382	0.768	0.787	95.1
1.48-1.51	3.9	0.577	6290	0.757	0.32	0.663	0.807	97.6
1.51-1.54	4.2	0.5	6335	0.829	0.266	0.569	0.839	98.5
1.54-1.57	4.6	0.423	6301	0.878	0.212	0.475	0.855	99
1.57-1.61	4.8	0.355	6366	0.913	0.175	0.397	0.891	99
1.61-1.65	4.8	0.316	6394	0.93	0.155	0.353	0.933	99.1
1.65-1.7	4.8	0.268	6362	0.949	0.132	0.3	0.952	99.3
1.7-1.75	4.8	0.224	6382	0.963	0.11	0.25	0.966	99.5
1.75-1.8	4.8	0.185	6390	0.974	0.091	0.207	1.013	99.4
1.8-1.87	4.9	0.146	6422	0.983	0.072	0.163	1.009	99.5
1.87-1.94	4.9	0.117	6435	0.989	0.058	0.131	1.032	99.6
1.94-2.03	4.9	0.088	6402	0.993	0.043	0.098	1.016	99.7
2.03-2.14	4.9	0.068	6449	0.996	0.034	0.077	0.989	99.8
2.14-2.27	5	0.057	6454	0.997	0.028	0.064	0.958	99.9
2.27-2.45	5	0.049	6458	0.997	0.024	0.054	0.887	100
2.45-2.69	5	0.042	6492	0.998	0.021	0.047	0.834	100
2.69-3.08	5	0.036	6502	0.998	0.018	0.04	0.841	100
3.08-3.88	5	0.033	6549	0.998	0.016	0.036	0.897	100
3.88-50	4.8	0.038	6662	0.995	0.019	0.043	1.264	99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.43→28.51 Å / SU ML: 0.1285 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1889	5864	4.94 %
R_work	0.1596	112775	-
obs	0.1611	118639	91.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.99 Å²

Refinement step

Cycle: LAST / Resolution: 1.43→28.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5605	0	96	887	6588

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0071	6154
X-RAY DIFFRACTION	f_angle_d	0.9396	8412
X-RAY DIFFRACTION	f_chiral_restr	0.0827	899
X-RAY DIFFRACTION	f_plane_restr	0.0079	1094
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3197	2277

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 (%)
1.43-1.45	0.2284	28	0.2447	705	X-RAY DIFFRACTION	17.23
1.45-1.46	0.2647	84	0.2375	1615	X-RAY DIFFRACTION	40.18
1.46-1.48	0.238	143	0.223	2715	X-RAY DIFFRACTION	66.95
1.48-1.5	0.2381	181	0.2124	3302	X-RAY DIFFRACTION	80.25
1.5-1.52	0.2216	183	0.2055	3488	X-RAY DIFFRACTION	86.27
1.52-1.54	0.2005	179	0.1977	3678	X-RAY DIFFRACTION	89.78
1.54-1.56	0.2338	189	0.1965	3770	X-RAY DIFFRACTION	92.93
1.56-1.59	0.1931	196	0.1906	3865	X-RAY DIFFRACTION	95.24
1.59-1.61	0.2038	193	0.1802	3944	X-RAY DIFFRACTION	96.73
1.61-1.64	0.2193	214	0.1765	3938	X-RAY DIFFRACTION	97.65
1.64-1.67	0.221	185	0.1753	4105	X-RAY DIFFRACTION	98.33
1.67-1.7	0.2215	209	0.1696	4004	X-RAY DIFFRACTION	99.2
1.7-1.73	0.1914	192	0.1717	4071	X-RAY DIFFRACTION	99.42
1.73-1.76	0.1954	219	0.169	4031	X-RAY DIFFRACTION	98.95
1.76-1.8	0.207	191	0.1684	4049	X-RAY DIFFRACTION	99.09
1.8-1.84	0.1825	227	0.1736	4047	X-RAY DIFFRACTION	99.42
1.84-1.89	0.2122	234	0.1767	4013	X-RAY DIFFRACTION	99.46
1.89-1.94	0.2216	199	0.1712	4109	X-RAY DIFFRACTION	99.49
1.94-2	0.2014	201	0.1652	4044	X-RAY DIFFRACTION	99.55
2-2.06	0.1963	223	0.1549	4053	X-RAY DIFFRACTION	99.63
2.06-2.14	0.176	233	0.1575	4098	X-RAY DIFFRACTION	99.7
2.14-2.22	0.1818	226	0.1549	4068	X-RAY DIFFRACTION	99.74
2.22-2.32	0.2047	213	0.1594	4135	X-RAY DIFFRACTION	99.86
2.32-2.45	0.1957	232	0.1621	4009	X-RAY DIFFRACTION	99.81
2.45-2.6	0.1915	196	0.1614	4159	X-RAY DIFFRACTION	99.77
2.6-2.8	0.1957	228	0.1663	4073	X-RAY DIFFRACTION	99.81
2.8-3.08	0.1867	211	0.1602	4117	X-RAY DIFFRACTION	99.82
3.08-3.53	0.1916	225	0.1501	4148	X-RAY DIFFRACTION	99.98
3.53-4.44	0.1585	223	0.1287	4130	X-RAY DIFFRACTION	99.89
4.44-28.51	0.147	207	0.1407	4292	X-RAY DIFFRACTION	99.49

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	0.0545749454672	0.0420051102357	0.00303573814081	0.101161897776	0.0238362704937	0.0127744879636	-0.0491335596534	0.184000652682	0.105127723561	-0.188847767646	0.0323676765932	0.0818894580082	-0.310759381409	-0.0641559368668	-0.00122412797696	0.24077524372	0.0553081914928	-0.0385252314863	0.202820542914	0.050762858853	0.153450525347	-53.3397798266	-12.3171921118	13.8424603904
2	0.107613104316	0.0822590366778	0.0994994464856	0.264997049494	0.0775395803007	0.10441427161	0.00560041790682	0.0477349346286	-0.0276817115732	-0.0212249824878	-0.0368254690147	0.0906252144425	-0.0124315606336	-0.0989817469524	0.00489244036355	0.0805546557734	0.00568613170835	-0.00915963104237	0.127247276016	-0.0336480345911	0.0906428431836	-56.5156007636	-25.9324695085	21.5874030193
3	0.127666441652	-0.0352745512879	0.0332878936485	0.287141626531	-0.0266822742617	0.0314930906715	-0.0109068848661	-0.0542080537341	-0.0743195611856	0.176177765889	-0.00897592998992	-0.0908848447742	0.0862551376001	-0.0160229917327	-0.0387567286295	0.165829224498	-0.0221770705802	-0.0286741215253	0.0726046317389	0.0126992975974	0.10799712376	-41.0887358023	-38.0741675723	44.2178473817
4	0.388635104145	0.0222158079803	0.13598668667	0.479215374741	0.0231881521918	0.682278346404	0.00804414685661	0.0267164736483	0.0161079180784	0.0501161444845	-0.0477098503999	0.0480172893912	0.0127622423099	-0.1013590715	-0.0415998787313	0.0723641874529	-0.0103897131497	0.00514743417254	0.0876190143688	-0.0219481942366	0.0936099233054	-51.9637741931	-24.5886978003	31.3943152725
5	0.0428105554691	-0.0253461150567	-0.0693251238681	0.0556472092872	0.0415246025596	0.0761495807752	-0.102391583654	0.0771831739673	-0.0797341800289	-0.274832688373	0.0266781203772	-0.086332980608	0.192197353777	0.0289406743361	1.12850702354E-5	0.246838948457	-0.00846054791198	0.0417856308884	0.126344235368	-0.0023423306406	0.142258426558	-8.53790579137	-33.0819575566	4.83923420933
6	0.391136122646	0.10911883132	-0.197606689089	0.433645915024	-0.27727326246	0.177584758823	0.167076327183	-0.139815713033	0.253893712433	-0.162249710884	-0.0733266262464	-0.0838441708869	-0.0297889311173	0.151270682853	0.0656970029257	0.0313171239721	-0.0838690608571	0.0165700669158	0.177137286032	-0.0602233498219	0.127565181356	-11.3011426656	-12.1580857846	20.5917507484
7	0.10530139491	0.0446556408771	-0.104746529296	0.104320967365	0.00472248532349	0.101245622852	0.0802004278977	-0.0487422528274	0.113567098807	0.0145627881045	0.0558546924581	0.103780330849	-0.159910063065	0.130506338267	0.0239521179641	0.124451517206	-0.0171269155305	0.0439022611869	0.11776635971	-0.00997009886397	0.146985065502	-23.6619350995	-10.0425868671	32.0921373805
8	0.22742068001	-0.0335739523147	-0.252940433534	0.204939424485	-0.0330772850961	0.292970596268	0.0970647007318	-0.0506781952343	0.179204432971	-0.15182697141	0.044952934357	-0.0768029303031	-0.109836203003	0.0655316523718	0.0275595827731	0.134244817407	-0.0382067234174	0.0437724375669	0.144172036725	-0.00574197284521	0.153727282965	-9.54576949792	-11.2323469761	14.1598507459
9	0.160767221327	-0.154223761959	4.20828602511E-5	0.173347448925	0.133216623165	0.295124153535	-0.17039415182	-0.16346216014	-0.195311348753	0.26490248987	0.199477820583	-0.11779641392	0.352377604806	0.280618002027	-0.00227960838315	-0.0631419055478	0.0176748255443	-0.0744580326414	0.349335842556	-0.0277767973445	0.124913980185	-4.84369865816	-23.051034544	30.4237732
10	0.0109019114476	0.0091991235555	-0.0253072043152	0.0246145788329	-0.0255123069316	0.0297894670185	-0.133946983801	-0.233350869154	-0.0813070172172	-0.0492247959361	0.0259627811249	-0.0259784252033	0.127171261287	0.0905693594186	-0.00141859218728	0.103894628154	-0.0107294514563	0.0166174522226	0.148740278604	0.0309776293394	0.132059130627	-14.2674141994	-33.0489542731	24.8772179536
11	0.00138258326899	-0.0297732599168	0.0236962532108	0.0497106335295	-0.043102995871	0.0462307655183	-0.0390820214412	0.0350413830814	-0.193169828718	0.0543746884012	0.06130341531	0.0409369262542	0.149546669826	0.141440956086	2.60973058721E-5	0.106528535924	0.0369378990361	-0.0141042905185	0.198037677826	0.00870571260251	0.129711706503	-16.9530721038	-27.8148668067	32.5726511404
12	0.143853630983	0.0327634017531	-0.179499202149	0.0578189814355	0.0167817338675	0.14987817393	-0.098447032419	-0.107730223474	-0.0630356519512	-0.105648136843	0.066208620731	-0.0175222392265	0.0884559735089	0.00524071296065	-0.0128863326649	0.129482391915	-0.000295925639688	0.00930159504611	0.114239497994	0.031886511029	0.111643744399	-11.7543521984	-29.7733947524	15.5819935731

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 31 through 50 )	A	A	31 - 50	1 - 20
2	2	chain 'A' and (resid 51 through 106 )	A	A	51 - 106	21 - 76
3	3	chain 'A' and (resid 107 through 189 )	A	A	107 - 189	77 - 159
4	4	chain 'A' and (resid 190 through 388 )	A	A	190 - 388	160 - 358
5	5	chain 'B' and (resid 30 through 71 )	B	N	30 - 71	1 - 42
6	6	chain 'B' and (resid 72 through 125 )	B	N	72 - 125	43 - 96
7	7	chain 'B' and (resid 126 through 189 )	B	N	126 - 189	97 - 160
8	8	chain 'B' and (resid 190 through 265 )	B	N	190 - 265	161 - 236
9	9	chain 'B' and (resid 266 through 294 )	B	N	266 - 294	237 - 265
10	10	chain 'B' and (resid 295 through 314 )	B	N	295 - 314	266 - 285
11	11	chain 'B' and (resid 315 through 337 )	B	N	315 - 337	286 - 308
12	12	chain 'B' and (resid 338 through 388 )	B	N	338 - 388	309 - 359

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 903 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 903 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi