PDB-6w33: Crystal Structure of Class A Beta-lactamase from Bacillus cereus ...

ID or keywords:

Entry

Database: PDB / ID: 6w33

Title

Crystal Structure of Class A Beta-lactamase from Bacillus cereus in the Complex with the Beta-lactamase Inhibitor Clavulanate

Components

Beta-lactamase

Keywords

HYDROLASE / Beta-lactamases / Antibiotic Resistant / inhibitor / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Class A Beta-lactamase from Bacillus cereus in the Complex with the Beta-lactamase Inhibitor Clavulanate
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Mar 8, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 25, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6w33.cif.gz	269.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6w33.ent.gz	180 KB	Display	PDB format
PDBx/mmJSON format	6w33.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6w33_validation.pdf.gz	488 KB	Display	wwPDB validaton report
Full document	6w33_full_validation.pdf.gz	492.4 KB	Display
Data in XML	6w33_validation.xml.gz	23.6 KB	Display
Data in CIF	6w33_validation.cif.gz	32.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w3/6w33 ftp://data.pdbj.org/pub/pdb/validation_reports/w3/6w33	HTTPS FTP

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Related structure data

Related structure data	3qhyS S: Starting model for refinement
Similar structure data	5a92-d 4hbu-d 4pm5-d 4a5r-1 6b1y-2 4xtz-1 5toy-1 2zq9-d 1iys-d 2y91-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: IDP97250

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#164 - Aug 2013 Serotonin Receptor similarity (5) #29 - May 2002 Penicillin-binding Proteins similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (2)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	42.728, 43.643, 72.404
Angle α, β, γ (deg.)	85.081, 88.250, 86.677
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

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Protein , 1 types, 2 molecules AB

#1: Protein	Beta-lactamase Mass: 31050.938 Da / Num. of mol.: 2 / Mutation: A274T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria) Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: bla, EJ379_12650 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold References: UniProt: A0A5B7VP54, UniProt: Q81DA0*PLUS, beta-lactamase

#1: Protein

Beta-lactamase

Mass: 31050.938 Da / Num. of mol.: 2 / Mutation: A274T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: bla, EJ379_12650 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: A0A5B7VP54, UniProt: Q81DA0*PLUS, beta-lactamase

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Non-polymers , 6 types, 205 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.14 Å³/Da / Density % sol: 42.48 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Magnesium chloride, 0.1 M MES pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 22, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. obs: 43737 / % possible obs: 98.9 % / Redundancy: 6 % / B_iso Wilson estimate: 29.47 Å² / CC_1/2: 0.975 / R_merge(I) obs: 0.128 / Net I/σ(I): 17
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.581 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 2120 / CC_1/2: 0.852 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBID 3QHY

3qhy

Resolution: 1.85→37.13 Å / SU ML: 0.2394 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.3782

	R_factor	Num. reflection	% reflection
R_free	0.2165	2242	5.13 %
R_work	0.1836	-	-
obs	0.1853	43702	98.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 45.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→37.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4056	0	20	195	4271

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	4177
X-RAY DIFFRACTION	f_angle_d	0.8474	5650
X-RAY DIFFRACTION	f_chiral_restr	0.053	643
X-RAY DIFFRACTION	f_plane_restr	0.0054	729
X-RAY DIFFRACTION	f_dihedral_angle_d	15.0487	2540

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 (%)
1.85-1.89	0.3288	114	0.2804	2447	X-RAY DIFFRACTION	92.32
1.89-1.93	0.2532	140	0.256	2548	X-RAY DIFFRACTION	97.85
1.93-1.98	0.3017	167	0.2366	2603	X-RAY DIFFRACTION	99.25
1.98-2.04	0.2756	120	0.2224	2646	X-RAY DIFFRACTION	99.1
2.04-2.1	0.2476	132	0.2073	2571	X-RAY DIFFRACTION	98.4
2.1-2.16	0.2664	130	0.209	2631	X-RAY DIFFRACTION	99.71
2.16-2.24	0.2426	143	0.2067	2613	X-RAY DIFFRACTION	98.99
2.24-2.33	0.2694	134	0.2083	2580	X-RAY DIFFRACTION	98.4
2.33-2.44	0.2571	137	0.2018	2609	X-RAY DIFFRACTION	99.13
2.44-2.57	0.2739	121	0.2012	2656	X-RAY DIFFRACTION	98.93
2.57-2.73	0.2559	143	0.2009	2613	X-RAY DIFFRACTION	99.71
2.73-2.94	0.2661	142	0.2012	2588	X-RAY DIFFRACTION	99.16
2.94-3.23	0.2622	160	0.2046	2569	X-RAY DIFFRACTION	98.52
3.23-3.7	0.2439	130	0.1723	2650	X-RAY DIFFRACTION	99.82
3.7-4.66	0.1527	155	0.1496	2561	X-RAY DIFFRACTION	98.44
4.66-37.13	0.1571	174	0.147	2575	X-RAY DIFFRACTION	98.71

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	2.02212057958	-1.09050646516	3.99675850456	7.01277970651	-3.56078445747	2.98479116347	0.410301622414	1.78720847508	0.256185064588	-1.27842445149	0.278921053185	-0.562235610068	0.179258807233	0.740797696815	-0.421249985312	0.507221701145	0.0235211636662	0.335198245972	0.33311270697	-0.0281727684777	0.666582943925	18.7559803522	2.73308682817	-13.5540082521
2	2.68327751856	0.164074029645	-0.403610648311	2.25204341172	0.516606692162	1.44647387743	-0.108156081853	0.221633337234	0.244953139022	-0.46124015168	0.14934274929	-0.194303249364	-0.0271589297095	0.05780938535	-0.00976361587732	0.269338558723	-0.0301273115773	0.0592310119077	0.148796789441	0.0170919281866	0.301804885751	2.13090425523	-0.841400225723	-7.09135661664
3	1.10198688311	-0.905928608331	2.67206855266	4.12388010168	-3.55531375391	6.97954443167	0.261078887718	-0.49404264341	-0.122664523016	0.391749681734	-0.00942490527476	1.13030246343	0.187866641518	-0.457646355144	-0.276202089198	0.312409314515	-0.0557228128496	0.148875891801	0.372213908998	-0.00409044580399	0.431985719543	-14.4089773051	-3.20203593718	15.2619060375
4	2.25441786186	0.435344621498	-1.19425143542	3.28763303876	-0.130912775731	4.09400870987	0.0292716851994	-0.477688615443	0.0167316332601	0.51739587614	-0.140790226455	0.216548926595	-0.0300108922555	0.0701951731661	0.0951460598993	0.281524424805	0.023453094533	0.0765717688721	0.302666589059	-0.00109718958496	0.28519411047	-5.73223651869	-2.40379026237	14.6968919589
5	2.12192829086	-0.0833149092782	-0.728287445855	3.15262731836	-0.686673607992	5.82066142402	-0.286816364769	0.104589187409	-0.281650570497	-0.137705801827	0.0838606042161	0.196565722823	0.30608192273	-0.463661026178	0.232829424259	0.241767907257	-0.0397418409809	0.082052016456	0.18763398023	-0.0163412906661	0.304783738173	-6.52144412462	-11.1654134147	-2.66283747265
6	3.4663262839	-0.47459499165	-0.859036757992	2.65429728495	-0.00209916781927	2.06921938088	-0.0845250058895	0.0299292878573	0.0454291352858	0.0596748553253	0.0601409249439	0.128056800253	0.00370141811345	-0.1186247884	-0.000125188356637	0.180801667286	-0.0367090466327	0.0304223546345	0.120082873785	0.00671972872794	0.210437388668	-3.96193593296	-1.23459946052	-2.51470349835
7	1.40900244882	0.367658768297	-0.254758137511	3.15606278613	-0.153991612104	1.10034924843	0.122747798398	-0.0755186326256	0.3135466052	0.00828238358564	0.0206835690511	-0.304483124014	-0.197306631204	0.119545741493	-0.151366807749	0.226678346318	0.000915874832131	0.00718866691386	0.14946121933	-0.0266969803655	0.331106878663	5.98732054929	7.1272395133	0.889092169369
8	3.8220553518	-1.23021214766	0.265002020363	4.94525565104	-0.0243505394683	2.19543098362	0.0981726965169	0.0684659685863	0.157010136503	-0.239243781298	0.020975789192	-0.615773074961	0.216209576309	0.227736582808	-0.119576849235	0.15104948148	-0.0417709581754	0.003681548044	0.216797732583	-0.00564684596422	0.310766024854	9.80671535415	1.38465838478	-3.06856489674
9	4.2397089644	-1.83872441682	2.71787659693	3.75239394611	-3.10786912152	3.71792677501	0.0313225799271	0.280720980894	0.251889842202	-0.467155483302	0.0672582157052	-0.547647309681	-0.16300566621	-0.250835753151	0.0670483141699	0.367700145384	-0.0264801021132	0.140296212686	0.137257358862	-0.0295255228539	0.52231179149	13.3481359416	8.59886008407	-6.80754593133
10	5.30609088998	0.0033503431684	-1.47532945807	4.91891202998	1.75554219901	5.29456535046	-0.373757077377	0.828700861453	-0.728961182316	-0.915769596141	0.323720040566	-0.618218351969	0.743334174315	0.644412561004	-0.0307013162827	0.685604186283	0.039575699307	0.116905520323	0.474400773421	-0.121316405199	0.336547522098	24.5904785516	-27.1671327209	-51.0614218787
11	2.62273783301	-1.36593504663	-4.45710872753	2.58566282699	2.73993827269	7.83778446547	0.0716560806593	-0.143372353508	0.233084283913	0.0544940055895	0.224546741041	-0.201870181505	-0.0175326691188	0.480787887297	-0.240672983197	0.385010936739	-0.0132962500964	0.0165571095238	0.289834147749	-0.00762446209207	0.2624124477	16.5103759772	-15.3310295233	-28.9791938031
12	3.82596470623	0.232447181744	-2.65788893463	3.80010728375	0.921102897898	4.62449911384	-0.629796212095	0.862513154403	-1.03817722024	0.465965761751	-0.13078688802	0.142732474616	1.55249983221	-0.000238470940846	0.338972106915	0.790086983198	0.0339801115825	0.195088125016	0.388840035903	-0.0746358381531	0.368176204503	18.6528144794	-28.165524965	-37.7385668108
13	5.14612736036	-3.90628890405	-3.46485993954	7.29971479159	0.444485067957	8.29054574244	-0.0766034024374	0.352803423758	-1.54766287331	-0.378458994809	-0.236507792623	-0.349717399767	2.18946061511	-0.177497756776	0.370557964681	0.960264304739	-0.0334452458855	0.206370782361	0.453816689104	-0.065454565629	0.553229591707	22.9158477661	-32.9239071615	-44.4331653593

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 51 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 108 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 109 through 124 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 165 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 166 through 190 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 191 through 234 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 235 through 273 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 274 through 296 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 297 through 311 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 51 through 76 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 77 through 234 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 235 through 296 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 297 through 311 )

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