PDB-2wuq: Crystal structure of BlaB protein from Streptomyces cacaoi

ID or keywords:

Entry

Database: PDB / ID: 2wuq

Title

Crystal structure of BlaB protein from Streptomyces cacaoi

Components

BETA-LACTAMASE REGULATORY PROTEIN BLAB

Keywords

TRANSCRIPTION / CLASS A BETA-LACTAMASE FOLD / TRANSCRIPTION REGULATION / BETA-LACTAMASE INDUCTION / RESISTANCE MECHANISM

Function / homology

Function and homology information

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

Biological species

STREPTOMYCES CACAOI (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Dandois, S. / Herman, R. / Sauvage, E. / Charlier, P. / Joris, B. / Kerff, F.

Citation

Journal: To be Published
Title: The Crystal Structure of Blab Protein from Streptomyces Cacaoi
Authors: Dandois, S. / Moutzourelis, G. / Herman, R. / Sauvage, E. / Charlier, P. / Joris, B. / Kerff, F.

History

Deposition	Oct 7, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 13, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2wuq.cif.gz	229.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2wuq.ent.gz	188.8 KB	Display	PDB format
PDBx/mmJSON format	2wuq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wu/2wuq ftp://data.pdbj.org/pub/pdb/validation_reports/wu/2wuq	HTTPS FTP

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Related structure data

Related structure data	1dy6S S: Starting model for refinement
Similar structure data	5i7o-2 5i7h-2 2qe2-2 4khr-2 5i6d-2 6j1i-d 5i6d-1 4x9k-1 6nmx-1 4tlv-1 Search similar-shape structures by Omokage search (details) 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 REGULATORY PROTEIN BLAB

B: BETA-LACTAMASE REGULATORY PROTEIN BLAB

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	54.140, 94.580, 61.380
Angle α, β, γ (deg.)	90.00, 99.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	BETA-LACTAMASE REGULATORY PROTEIN BLAB / BLAB Mass: 34677.055 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-312 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CACAOI (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): TK24 / References: UniProt: P33652
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.56 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979738
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979738 Å / Relative weight: 1
Reflection	Resolution: 1.8→47.3 Å / Num. obs: 56421 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / B_iso Wilson estimate: 0 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 10.4
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 5.7 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DY6

1dy6

Resolution: 1.8→47.3 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.939 / SU B: 4.95 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20099	2860	5.1 %	RANDOM
R_work	0.16055	-	-	-
obs	0.1626	53512	99.91 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.969 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.19 Å²	0 Å²	0.16 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→47.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4305	0	12	420	4737

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	4439
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.423	1.975	6047
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.353	5	564
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.698	22.304	204
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.841	15	713
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.769	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	700
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3400
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	2131
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	2986
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	343
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.176	0.2	66
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.159	0.2	17
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.026	1.5	2877
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.521	2	4514
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.441	3	1712
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.004	4.5	1529
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	217	-
R_work	0.224	3924	-
obs	-	-	99.64 %

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	0.8158	-0.736	-0.0558	2.4031	-0.1741	0.8095	0.028	-0.075	-0.1925	0.1058	-0.0101	0.0089	0.19	-0.1354	-0.0179	-0.0321	-0.0256	-0.0242	-0.0347	0.0286	-0.0113	42.643	32.545	53.974
2	1.1366	0.3604	-0.9094	0.9579	-0.0289	1.4438	0.06	-0.0163	0.0565	0.1056	-0.0321	-0.0575	-0.0602	0.0354	-0.0279	-0.0359	-0.0009	-0.0363	-0.0606	-0.0101	-0.034	48.963	62.195	56.033
3	7.2494	-1.2119	1.1726	2.7185	0.1367	5.987	-0.0493	-0.0254	-0.1105	0.1107	0.0503	-0.0488	0.1541	0.1642	-0.001	0.134	-0.0016	-0.007	0.0431	0.0043	-0.0105	41.215	50.973	65.542
4	38.9197	-19.8763	8.2753	18.2762	11.9201	33.8443	0.849	-0.6298	0.1996	1.6044	0.0744	-0.994	-1.4948	2.037	-0.9234	0.0011	0.0005	0.0019	-0.0007	-0.0005	-0.0014	56.115	42.373	69.576
5	1.3988	-0.1747	0.7364	1.2031	-0.4259	2.5069	-0.0351	-0.1971	0.0539	0.093	0.0421	0.0943	0.1289	-0.3008	-0.007	-0.0629	-0.0076	-0.0058	-0.0518	-0.0192	-0.0245	34.598	44.907	54.475
6	28.8841	21.6279	15.6571	29.8147	7.7399	9.6525	1.1117	-0.5387	0.0565	0.1989	-0.4814	1.9594	0.6119	-0.5842	-0.6303	-0.0252	-0.0868	-0.0104	-0.0604	-0.0315	-0.0038	25.616	49.38	54.7
7	1.0787	-0.4812	0.0515	1.1111	-0.2027	0.811	0	-0.0163	0.0132	-0.0056	-0.0448	-0.096	0.0228	0.0674	0.0448	-0.0592	-0.0069	-0.03	-0.0536	0.0058	-0.0261	45.188	41.803	47
8	21.8587	-1.3111	30.251	35.9549	5.4176	43.3231	-0.2528	-0.6935	-0.2774	0.4147	-0.0246	1.4177	-0.06	-2.1033	0.2773	0.0513	0.0231	-0.0223	-0.0528	-0.0735	0.1632	29.463	29.213	40.673
9	4.2517	-0.5853	2.4159	2.198	-0.5525	1.8763	0.3205	0.5514	-0.4349	-0.3443	-0.1851	0.0329	0.3697	0.1039	-0.1354	-0.0193	0.0378	-0.0168	0.0747	-0.077	-0.0245	66.126	37.478	23.373
10	1.1552	-0.3833	-0.5514	0.9352	0.0951	1.1493	0.0472	0.073	0.0742	-0.0055	-0.0461	-0.006	-0.1488	-0.0252	-0.0012	-0.0571	-0.0145	-0.0333	-0.0463	0.0128	-0.026	59.447	64.004	37.234
11	2.2011	0.0075	0.7386	2.2559	0.2041	2.389	-0.0643	0.1667	0.0946	-0.097	-0.0191	-0.1061	-0.0486	0.1158	0.0834	0.0142	-0.0407	-0.0175	0.0117	0.0373	0.0201	67.375	66.115	26.375
12	6.1091	-1.761	2.3286	4.7312	9.3566	24.6958	0.3276	-0.4504	-0.2069	-0.2604	-0.3262	0.3645	-0.0038	-1.0963	-0.0014	-0.0695	-0.053	0.0047	0.0255	0.0387	-0.0435	51.912	59.674	18.111
13	1.3514	-1.0122	1.2527	1.3329	-0.7439	2.3751	-0.0581	0.0656	0.1016	-0.0502	-0.0479	-0.1424	-0.0125	0.0679	0.106	-0.0653	-0.0158	0.0052	-0.0249	0.0156	0.0041	68.066	54.898	27.23
14	9.3806	3.724	-1.0865	5.8928	-0.3654	2.1288	-0.1576	-0.0465	0.0907	-0.1408	0.045	-0.3937	-0.1585	0.2418	0.1125	-0.0719	0.0027	-0.0441	-0.041	0.0127	-0.0136	72.131	57.016	39.421
15	2.5388	0.1215	1.0756	1.4786	-0.4857	1.6326	-0.0359	0.0822	-0.0497	0.034	0.0828	0.0969	0.039	-0.1092	-0.0469	-0.0891	-0.0031	-0.0243	-0.0343	0.0065	-0.0312	60.084	45.087	33.425
16	9.2553	-1.4727	0.2472	6.8345	-1.134	5.3534	-0.0794	0.401	-0.8999	-0.0539	-0.0709	-0.2615	0.567	0.2165	0.1503	0.032	0.0188	-0.0058	-0.0509	-0.037	0.0657	69.548	34.541	30.671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 4
2	X-RAY DIFFRACTION	2	A	5 - 126
3	X-RAY DIFFRACTION	3	A	127 - 146
4	X-RAY DIFFRACTION	4	A	177 - 186
5	X-RAY DIFFRACTION	5	A	187 - 209
6	X-RAY DIFFRACTION	6	A	210
7	X-RAY DIFFRACTION	6	A	218 - 220
8	X-RAY DIFFRACTION	7	A	221 - 310
9	X-RAY DIFFRACTION	8	A	311 - 315
10	X-RAY DIFFRACTION	9	B	1 - 33
11	X-RAY DIFFRACTION	10	B	34 - 118
12	X-RAY DIFFRACTION	11	B	119 - 144
13	X-RAY DIFFRACTION	12	B	145 - 147
14	X-RAY DIFFRACTION	12	B	171 - 178
15	X-RAY DIFFRACTION	13	B	179 - 210
16	X-RAY DIFFRACTION	14	B	218 - 236
17	X-RAY DIFFRACTION	15	B	237 - 299
18	X-RAY DIFFRACTION	16	B	300 - 312

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