PDB-7mqn: Crystal structure of class C beta lactamase from Rhodobacter spha...

ID or keywords:

Entry

Database: PDB / ID: 7mqn

Title

Crystal structure of class C beta lactamase from Rhodobacter sphaeroides

Components

Beta-lactamase

Keywords

HYDROLASE / beta-lactamase / AmpC / structural genomics / anti / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

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

Biological species

Rhodobacter sphaeroides 2.4.1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.21 Å

Authors

Chang, C. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of class C beta lactamase from Rhodobacter sphaeroides
Authors: Chang, C. / Tesar, C. / Endres, M. / Joachimiak, A.

History

Deposition	May 5, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2021	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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PDBx/mmCIF format	7mqn.cif.gz	284.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7mqn.ent.gz	229.8 KB	Display	PDB format
PDBx/mmJSON format	7mqn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7mqn_validation.pdf.gz	439.2 KB	Display	wwPDB validaton report
Full document	7mqn_full_validation.pdf.gz	440.2 KB	Display
Data in XML	7mqn_validation.xml.gz	28.3 KB	Display
Data in CIF	7mqn_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mq/7mqn ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mqn	HTTPS FTP

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Related structure data

Related structure data	6njkS S: Starting model for refinement
Similar structure data	3o86-1 4u0t-6 5gsc-2 6tzh-3 1ke0-2 5e2g-1 5chj-1 4kg5-4 6yeo-3 5za2-2 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: CSGID-IDP97225

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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)

Deposited unit

A: Beta-lactamase

B: Beta-lactamase

hetero molecules

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

1

A: Beta-lactamase

hetero molecules

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

2

B: Beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	165.978, 72.090, 115.280
Angle α, β, γ (deg.)	90.000, 132.790, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Beta-lactamase Mass: 37937.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria) Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: ampC, RSP_3749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3IVS9, beta-lactamase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.34 Å³/Da / Density % sol: 63.12 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M Phosphate-citrate pH 4.2, 1.6M Sodium phosphate dibasic, 0.4M potassium phosphate monobasic

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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: 0.97913 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 22, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97913 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 49810 / % possible obs: 98.8 % / Redundancy: 3.7 % / B_iso Wilson estimate: 30.19 Å² / R_merge(I) obs: 0.119 / R_pim(I) all: 0.069 / R_rim(I) all: 0.138 / Χ²: 0.829 / Net I/σ(I): 7.1 / Num. measured all: 185389

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
2.2-2.24	3.8	0.665	2472	0.708	0.388	0.772	0.772	99
2.24-2.28	3.8	0.529	2464	0.686	0.313	0.617	0.934	99
2.28-2.32	3.8	0.514	2502	0.861	0.3	0.597	0.752	99.1
2.32-2.37	3.7	0.419	2470	0.87	0.246	0.487	0.737	99
2.37-2.42	3.8	0.363	2470	0.885	0.211	0.421	0.769	98.4
2.42-2.48	3.8	0.328	2493	0.893	0.191	0.381	0.787	98.6
2.48-2.54	3.7	0.304	2444	0.915	0.178	0.353	0.805	99
2.54-2.61	3.7	0.253	2507	0.931	0.149	0.294	0.786	99.4
2.61-2.69	3.7	0.221	2491	0.938	0.13	0.258	0.834	99.4
2.69-2.77	3.5	0.196	2452	0.941	0.119	0.23	0.859	97.7
2.77-2.87	3.5	0.177	2461	0.957	0.107	0.208	0.897	97.6
2.87-2.99	3.9	0.144	2486	0.971	0.082	0.166	0.877	99.4
2.99-3.12	3.8	0.131	2506	0.973	0.074	0.151	0.886	99.5
3.12-3.29	3.8	0.116	2518	0.977	0.066	0.134	0.952	99.5
3.29-3.49	3.8	0.104	2487	0.98	0.059	0.12	0.945	99.3
3.49-3.76	3.7	0.095	2523	0.984	0.054	0.11	0.897	99.1
3.76-4.14	3.4	0.089	2444	0.972	0.054	0.104	0.838	97.2
4.14-4.74	3.9	0.084	2523	0.983	0.047	0.096	0.739	99.5
4.74-5.97	3.8	0.083	2551	0.983	0.046	0.095	0.624	99.6
5.97-50	3.6	0.123	2546	0.958	0.072	0.143	0.913	97.4

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
SBC-Collect		data collection
PHENIX	1.19_4092	refinement
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6NJK

6njk

Resolution: 2.21→42.45 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2197	2261	4.94 %
R_work	0.182	43491	-
obs	0.1839	45752	90.57 %

Solvent computation

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

Displacement parameters

B_iso max: 128.05 Å² / B_iso mean: 33.7265 Å² / B_iso min: 15.34 Å²

Refinement step

Cycle: final / Resolution: 2.21→42.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5348	0	30	386	5764
B_iso mean	-	-	37.53	34.67	-
Num. residues	-	-	-	-	702

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.21-2.25	0.2858	69	0.2112	1491	1560	49
2.25-2.31	0.2584	59	0.2089	1880	1939	62
2.31-2.36	0.2923	132	0.2156	2247	2379	77
2.36-2.43	0.2303	112	0.1969	2644	2756	88
2.43-2.5	0.2377	152	0.1999	2775	2927	93
2.5-2.58	0.2455	157	0.2098	2928	3085	98
2.58-2.67	0.2521	158	0.2033	2924	3082	98
2.67-2.78	0.2565	142	0.2156	2928	3070	98
2.78-2.91	0.2798	182	0.2161	2866	3048	97
2.91-3.06	0.2456	177	0.2092	2947	3124	99
3.06-3.25	0.2667	152	0.2	2977	3129	99
3.25-3.5	0.2059	151	0.1803	2994	3145	99
3.5-3.85	0.2064	143	0.1582	2970	3113	98
3.85-4.41	0.161	142	0.1434	2950	3092	97
4.41-5.55	0.1753	122	0.1479	3026	3148	99
5.55-42.45	0.2011	211	0.1851	2944	3155	96

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	0.3731	-0.1003	-0.2048	0.4171	0.2603	0.3081	-0.1905	-0.703	-0.0248	0.5594	0.2421	-0.3072	0.5319	0.7357	0.3832	0.3341	0.1453	-0.3293	0.4614	0.0888	0.2945	-16.8447	33.6967	90.629
2	1.0402	0.2739	-0.5303	0.7898	0.1487	1.3206	-0.1743	0.0288	-0.0989	0.0938	0.0019	0.0652	0.1667	-0.0289	-0.0012	0.2022	0.0213	0.0087	0.1743	0.0167	0.1872	-34.0271	32.5878	73.6859
3	-0.0089	-0.0255	-0.0343	0.0213	0.0277	0.0824	-0.3058	-0.1785	-0.4807	0.2885	0.1738	-0.1478	0.3375	-0.0179	0.0003	0.5572	0.0673	0.1842	0.3533	0.1123	0.4531	-24.6153	19.2935	66.0652
4	0.0906	0.0219	0.0926	0.0239	0.0457	0.183	-0.0369	-0.0833	-0.1674	0.0171	0.0154	-0.2396	0.1468	0.2404	0.0081	0.2823	0.1008	0.0084	0.306	0.0817	0.3271	-19.5401	28.2782	81.9664
5	0.9287	-0.1668	-0.7053	0.8406	-0.063	0.9943	0.1119	0.0702	0.1148	0.0242	0.0394	-0.0639	-0.0368	-0.0459	0.0045	0.1574	-0.0225	-0.0292	0.1551	-0.0043	0.1785	-8.6073	38.1866	47.4983
6	0.3294	-0.2289	0.0408	0.3264	0.1524	0.4347	0.0917	-0.0432	0.0631	-0.0085	-0.0497	-0.0961	0.0007	0.1292	-0	0.2134	-0.0259	0.0187	0.2273	-0.0209	0.2377	1.8915	35.0093	45.0894
7	0.256	0.1463	-0.0966	0.2364	-0.1385	0.1396	0.0643	-0.0106	0.5177	0.2146	0.2085	-0.0156	-0.3825	-0.1536	0.0817	0.3118	0.012	0.0491	0.1967	-0.0746	0.2884	-9.3654	50.9037	55.7821
8	0.0597	0.0103	0.0051	0.0242	0.02	-0.0081	-0.0873	0.001	0.3765	0.1744	0.2012	-0.1717	-0.481	0.275	0.0001	0.4607	-0.0556	0.0637	0.2972	0.0368	0.5088	-15.163	52.6452	56.0384
9	0.2954	-0.1662	-0.0246	0.0574	0.027	0.065	0.0197	-0.1893	0.1442	0.2766	0.0423	-0.193	-0.0828	0.1415	-0	0.3074	-0.0478	0.0073	0.2596	-0.0836	0.269	1.1918	43.6148	59.7821

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 29 through 68 )	A	29 - 68
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 308 )	A	69 - 308
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 309 through 328 )	A	309 - 328
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 329 through 379 )	A	329 - 379
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 29 through 188 )	B	29 - 188
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 189 through 268 )	B	189 - 268
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 269 through 308 )	B	269 - 308
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 309 through 328 )	B	309 - 328
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 329 through 379 )	B	329 - 379

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