PDB-7agz: BsrV no-histagged

ID or keywords:

Entry

Database: PDB / ID: 7agz

Title

BsrV no-histagged

Components

Broad specificity amino-acid racemase

Keywords

PEPTIDE BINDING PROTEIN / Broad spectrum / Racemase / peptidoglycan binding protein

Function / homology

Function and homology information

methionine racemase activity / ornithine racemase activity / arginine racemase activity / lysine racemase activity / amino-acid racemase / serine racemase activity / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding ...
Similarity search - Function

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.52 Å

Authors

Carrasco-Lopez, C. / Rojas-Altuve, A. / Espaillat, A. / Cava, F. / Hermoso, J.A.

Funding support

Spain,

Sweden, 2items

Citation

Journal: Comput Struct Biotechnol J / Year: 2021
Title: Binding of non-canonical peptidoglycan controls Vibrio cholerae broad spectrum racemase activity.
Authors: Espaillat, A. / Carrasco-Lopez, C. / Bernardo-Garcia, N. / Rojas-Altuve, A. / Klett, J. / Morreale, A. / Hermoso, J.A. / Cava, F.

History

Deposition	Sep 23, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 20, 2022	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7agz.cif.gz	359.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7agz.ent.gz	257.2 KB	Display	PDB format
PDBx/mmJSON format	7agz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7agz_validation.pdf.gz	464.4 KB	Display	wwPDB validaton report
Full document	7agz_full_validation.pdf.gz	473 KB	Display
Data in XML	7agz_validation.xml.gz	36.5 KB	Display
Data in CIF	7agz_validation.cif.gz	55.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ag/7agz ftp://data.pdbj.org/pub/pdb/validation_reports/ag/7agz	HTTPS FTP

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Related structure data

Related structure data	4beuS S: Starting model for refinement
Similar structure data	6xin-d 6duc-d 1i2c-1 0471 4hpx-d 3i8v-d 7jhw-d 3beq-d 5npf-d 1kfe-d 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

Deposited unit

A: Broad specificity amino-acid racemase

B: Broad specificity amino-acid racemase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	54.030, 82.090, 160.210
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Broad specificity amino-acid racemase / Broad spectrum racemase Mass: 42514.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: bsrV, VC_1312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KSE5, amino-acid racemase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.1 Å³/Da / Density % sol: 41.38 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Bis-Tris propane pH 7.5, 0.2 M Sodium Iodide, and 24% (p/v) of PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.516→51.2 Å / Num. obs: 111214 / % possible obs: 99.9 % / Redundancy: 7.2 % / B_iso Wilson estimate: 14.34 Å² / CC_1/2: 0.981 / R_merge(I) obs: 0.092 / R_pim(I) all: 0.036 / Net I/σ(I): 14
Reflection shell	Resolution: 1.516→1.57 Å / R_merge(I) obs: 0.562 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 10958 / CC_1/2: 0.819 / R_pim(I) all: 0.205

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PHENIX	1.18.2_3874	refinement
Aimless		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4beu

4beu

Resolution: 1.52→51.2 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2003	7979	7.18 %
R_work	0.1847	103073	-
obs	0.1858	111052	99.82 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.07 Å²

Refinement step

Cycle: LAST / Resolution: 1.52→51.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5904	0	44	703	6651

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0155	6114
X-RAY DIFFRACTION	f_angle_d	1.5627	8299
X-RAY DIFFRACTION	f_chiral_restr	0.0983	949
X-RAY DIFFRACTION	f_plane_restr	0.0139	1084
X-RAY DIFFRACTION	f_dihedral_angle_d	17.9331	2269

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 (%)
1.52-1.53	0.286	230	0.2722	3407	X-RAY DIFFRACTION	99.59
1.53-1.55	0.3027	273	0.2614	3381	X-RAY DIFFRACTION	99.73
1.55-1.57	0.3134	268	0.2587	3367	X-RAY DIFFRACTION	99.86
1.57-1.59	0.2706	261	0.2503	3430	X-RAY DIFFRACTION	99.76
1.59-1.61	0.2663	240	0.2427	3407	X-RAY DIFFRACTION	99.78
1.61-1.63	0.2894	262	0.2392	3406	X-RAY DIFFRACTION	99.81
1.63-1.66	0.2779	278	0.2325	3353	X-RAY DIFFRACTION	99.78
1.66-1.68	0.2596	261	0.2294	3440	X-RAY DIFFRACTION	99.81
1.68-1.71	0.2401	255	0.2228	3388	X-RAY DIFFRACTION	99.81
1.71-1.74	0.2181	255	0.2161	3416	X-RAY DIFFRACTION	99.81
1.74-1.77	0.2809	257	0.2202	3409	X-RAY DIFFRACTION	99.78
1.77-1.8	0.2206	271	0.2045	3410	X-RAY DIFFRACTION	99.81
1.8-1.83	0.2214	214	0.2046	3428	X-RAY DIFFRACTION	99.89
1.83-1.87	0.2386	242	0.2018	3455	X-RAY DIFFRACTION	99.86
1.87-1.91	0.2359	255	0.1955	3429	X-RAY DIFFRACTION	99.84
1.91-1.95	0.2239	248	0.1973	3425	X-RAY DIFFRACTION	99.78
1.95-2	0.207	277	0.1818	3447	X-RAY DIFFRACTION	99.81
2-2.06	0.196	274	0.1809	3391	X-RAY DIFFRACTION	99.92
2.06-2.12	0.1962	281	0.1748	3386	X-RAY DIFFRACTION	99.81
2.12-2.19	0.1818	275	0.1732	3432	X-RAY DIFFRACTION	99.81
2.19-2.26	0.1881	304	0.1712	3394	X-RAY DIFFRACTION	99.92
2.26-2.35	0.1943	269	0.1811	3442	X-RAY DIFFRACTION	99.92
2.35-2.46	0.1956	264	0.1848	3454	X-RAY DIFFRACTION	99.92
2.46-2.59	0.1922	276	0.1773	3443	X-RAY DIFFRACTION	99.84
2.59-2.75	0.1732	290	0.1769	3421	X-RAY DIFFRACTION	99.89
2.75-2.97	0.187	264	0.1777	3491	X-RAY DIFFRACTION	99.89
2.97-3.27	0.1805	271	0.1768	3484	X-RAY DIFFRACTION	99.84
3.27-3.74	0.1837	286	0.1586	3485	X-RAY DIFFRACTION	99.68
3.74-4.71	0.1625	299	0.1472	3530	X-RAY DIFFRACTION	99.87
4.71-51.2	0.1836	279	0.1844	3722	X-RAY DIFFRACTION	99.83

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	0.84579389145	-0.380535183802	-0.271365194287	0.262245959174	0.0621626691046	1.60011176414	-0.0159856710738	0.097703854357	-0.119215002706	-0.0547938987326	-0.0168697102175	-0.0250001826145	0.197404663531	0.17903521293	0.0132958886078	0.169054841902	0.029771608932	0.0149242126276	0.0948785719555	-0.00615464471891	0.146843353218	13.1323682092	32.3476127455	-7.850530818
2	1.67460512181	-0.132801870164	-0.56491398842	0.320943428236	0.19235562687	1.2527770863	-0.0343788399739	-0.196567240082	0.0543623515185	0.0987783249475	0.0113606128901	0.0174049076069	0.0641110613632	0.0500538792087	0.0271541486461	0.129029817487	-0.00121726579762	0.00696999998789	0.0911015187294	-0.021494113514	0.101659476993	4.311807257	39.8061430752	13.4188160325
3	0.993919238006	-0.293980081784	0.0691990564469	0.60135795274	-0.38387232791	1.64486776323	-0.0354358316911	0.0273217967134	0.103279014944	-0.0309555205207	-0.0107250593592	-0.0618511646674	-0.00172235158356	0.0676039153426	0.0365425427963	0.0870444647061	-0.00582535714297	0.00816294382603	0.0775739838228	0.00281867044621	0.0985898017627	10.4967846688	46.8339829911	-27.8028939143
4	1.30419035061	0.0516429089558	-0.72652072578	1.9453143695	0.271646955294	2.20789135871	-0.0284284570684	-0.0411989645334	0.0663541224379	0.00118433383456	0.0588919688074	-0.0842321049113	-0.0247308150252	0.110090322609	-0.0105430773537	0.088849392321	-0.00704233745455	0.0107873208441	0.132815044378	-0.0102721575733	0.0910562110954	9.8527780092	42.3266457657	-11.0985361776
5	1.53679670371	0.123052136818	0.697580880407	0.750790531375	0.184610274671	1.59031245962	0.09685809507	-0.148565178914	-0.0846027179354	0.137802189437	-0.020859797793	-0.0228946475682	0.180064947038	-0.200950795072	0.251862055673	0.13608972844	-0.0232822029672	0.00750087686816	0.0863248890547	-0.0130780958092	0.109808912907	-14.9958060989	31.9803938617	-14.9831227509
6	0.888162868898	0.0644786985087	-0.574336280921	0.588796727472	0.0915743606858	0.95079974211	-0.0358112836348	0.0488864058555	-0.0658644020746	-0.000223622935869	0.0293716407474	0.00607232014053	0.102441895471	-0.0260068866332	-0.00189136406917	0.119467574018	0.003846597893	-0.00593954393977	0.101949526621	-0.0139102977679	0.115475700219	-4.08530818468	28.6678989189	-32.3222776173
7	0.337023836966	0.00218647666078	-0.0845518829194	0.202429610417	0.133581098943	1.06103415396	0.00597277741983	0.0452355713876	0.0664389271507	-0.00618387834349	-0.00914156194416	0.0236818083727	-0.0467644410445	-0.0820302618584	-0.0241064736952	0.0913308827804	0.0110537705542	0.0115299791349	0.0630042155587	-0.00117246099775	0.123876301658	-9.77612995227	45.3183391157	-21.2136446305
8	0.786049472637	-0.0825771461362	-0.383456297614	0.14136502651	0.0801048951452	0.642011117386	0.00417816022208	0.0570605385464	0.0408529361735	0.00745884551512	-0.0210295596275	0.0924221233172	-0.0169122625138	-0.0801343573114	0.00322266692597	0.127752049421	0.00397872664255	0.0118861834894	0.16058050962	-0.011798933385	0.142860586461	-13.0484871907	40.9253743304	-13.1472529791

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 24 through 62 )	A	A	24 - 62	1 - 40
2	2	chain 'A' and (resid 63 through 278 )	A	A	63 - 278	41 - 258
3	3	chain 'A' and (resid 279 through 378 )	A	A	279 - 378	259 - 359
4	4	chain 'A' and (resid 379 through 409 )	A	A	379 - 409	360 - 390
5	5	chain 'B' and (resid 24 through 62 )	B	D	24 - 62	1 - 40
6	6	chain 'B' and (resid 63 through 165 )	B	D	63 - 165	41 - 144
7	7	chain 'B' and (resid 166 through 378 )	B	D	166 - 378	145 - 358
8	8	chain 'B' and (resid 379 through 411 )	B	D	379 - 411	359 - 392

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