PDB-5ewq: The crystal structure of an amidase family protein from Bacillus ...

ID or keywords:

Entry

Database: PDB / ID: 5ewq

Title

The crystal structure of an amidase family protein from Bacillus anthracis str. Ames

Components

Amidase

Keywords

HYDROLASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.57 Å

Authors

Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of an amidase family protein from Bacillus anthracis str. Ames
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Nov 20, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 9, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ewq.cif.gz	587.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5ewq.ent.gz	486 KB	Display	PDB format
PDBx/mmJSON format	5ewq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5ewq_validation.pdf.gz	459.3 KB	Display	wwPDB validaton report
Full document	5ewq_full_validation.pdf.gz	473.2 KB	Display
Data in XML	5ewq_validation.xml.gz	51.4 KB	Display
Data in CIF	5ewq_validation.cif.gz	69.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ew/5ewq ftp://data.pdbj.org/pub/pdb/validation_reports/ew/5ewq	HTTPS FTP

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Related structure data

Similar structure data	1crl-d 6ro8-d 4gv7-2 6hqd-2 2bzu-1 5g2o-d 3tyw-3 5ex6-3 4zzx-2 6s3h-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: ICSGID-DP05166 TargetTrack: CSGID-IDP05166

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Amidase

B: Amidase

C: Amidase

hetero molecules

173 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Amidase

hetero molecules

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

2

B: Amidase

hetero molecules

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

3

C: Amidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.390, 89.558, 89.600
Angle α, β, γ (deg.)	112.03, 106.64, 106.55
Int Tables number	1
Space group name H-M	P1

#1: Protein	Amidase / Amidase family protein / Glutamyl-tRNA(Gln) amidotransferase subunit A Mass: 57561.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Gene: gatA, GBAA_1921, AB163_14105, AB164_01390, AB165_02780, AB166_15195, AB167_02705, AB168_09340, AB169_26530, AB170_25470, AB171_03690, ADT20_23120, ADT21_23730, BASH2_03935 Plasmid: pMCSG7 / Cell line (production host): BL21(DE3)magic / Production host: Escherichia coli (E. coli) References: UniProt: Q81RW6, UniProt: A0A6L8P6E2*PLUS, amidase
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.92 Å³/Da / Density % sol: 57.84 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 24% (w/v) PEG1500, 20% (v/v) glycerol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97937, 0.97951

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97937	1
2	0.97951	1

Reflection

Resolution: 2.57→30.5 Å / Num. obs: 59854 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / B_iso Wilson estimate: 39.6 Å² / R_merge(I) obs: 0.015 / Net I/σ(I): 27.3

Reflection shell

Resolution: 2.57→2.61 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.729 / Mean I/σ(I) obs: 1.3 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.57→30.347 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2538	2915	5.23 %	Random selection
R_work	0.22	-	-	-
obs	0.2219	55724	91.42 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.57→30.347 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11340	0	12	80	11432

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11531
X-RAY DIFFRACTION	f_angle_d	0.521	15647
X-RAY DIFFRACTION	f_dihedral_angle_d	10.958	4212
X-RAY DIFFRACTION	f_chiral_restr	0.021	1813
X-RAY DIFFRACTION	f_plane_restr	0.002	2063

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 (%)
2.5701-2.6122	0.3717	50	0.2982	958	X-RAY DIFFRACTION	36
2.6122-2.6572	0.3124	85	0.3107	1507	X-RAY DIFFRACTION	54
2.6572-2.7055	0.3066	70	0.3232	2147	X-RAY DIFFRACTION	76
2.7055-2.7575	0.3706	82	0.3049	2530	X-RAY DIFFRACTION	91
2.7575-2.8137	0.3534	200	0.2907	2674	X-RAY DIFFRACTION	98
2.8137-2.8749	0.3228	177	0.2828	2666	X-RAY DIFFRACTION	98
2.8749-2.9417	0.31	127	0.2906	2733	X-RAY DIFFRACTION	98
2.9417-3.0152	0.2613	132	0.2829	2686	X-RAY DIFFRACTION	98
3.0152-3.0967	0.3111	112	0.2769	2820	X-RAY DIFFRACTION	98
3.0967-3.1877	0.281	166	0.2554	2630	X-RAY DIFFRACTION	98
3.1877-3.2904	0.3032	125	0.2574	2740	X-RAY DIFFRACTION	98
3.2904-3.4079	0.287	148	0.2418	2719	X-RAY DIFFRACTION	98
3.4079-3.5442	0.2794	133	0.2306	2719	X-RAY DIFFRACTION	98
3.5442-3.7052	0.26	200	0.2255	2706	X-RAY DIFFRACTION	99
3.7052-3.9002	0.2378	123	0.2033	2747	X-RAY DIFFRACTION	99
3.9002-4.1439	0.2455	150	0.1802	2692	X-RAY DIFFRACTION	99
4.1439-4.463	0.1784	190	0.1689	2679	X-RAY DIFFRACTION	99
4.463-4.9104	0.2134	181	0.1676	2676	X-RAY DIFFRACTION	99
4.9104-5.6171	0.2031	132	0.1762	2776	X-RAY DIFFRACTION	99
5.6171-7.0622	0.2516	152	0.1995	2733	X-RAY DIFFRACTION	99
7.0622-30.3493	0.2267	180	0.1808	2271	X-RAY DIFFRACTION	85

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	2.1202	0.1271	-0.2029	2.3795	0.2856	1.8345	-0.0987	0.5445	1.1386	-0.2894	0.1983	1.1756	-0.7573	-0.3507	0.0503	0.4792	0.2194	-0.0687	0.2707	0.0964	0.9256	-9.0597	5.4434	-10.8949
2	2.6124	0.6469	0.2414	2.6539	0.6535	2.0069	0.2583	-0.6365	0.4626	0.6256	-0.1937	0.5808	-0.5167	0.2006	0.0059	0.4989	-0.0001	0.0737	0.3293	-0.1227	0.3833	0.3847	0.4247	2.9889
3	2.9678	1.207	0.3858	2.0353	0.4036	1.7949	0.3638	-1.0209	-0.2179	0.7981	-0.3438	-0.0696	-0.1976	0.5395	-0.0388	0.6003	-0.1651	-0.0218	0.6406	-0.0509	0.2378	7.19	-4.7369	7.3512
4	3.1547	0.0479	-0.8526	3.6308	-0.6313	3.5263	0.0768	-1.3453	0.0435	1.0205	0.1895	0.2822	0.1742	-0.6191	-0.2431	0.6077	-0.0367	0.1181	0.7987	0.0215	0.3163	21.1746	51.9256	2.165
5	1.3024	0.7431	-0.5981	2.2058	-1.1045	2.1821	0.02	-1.0207	-0.4616	0.8498	-0.0226	0.7968	0.2101	-0.6825	-0.8935	0.3526	-0.4305	0.4859	0.8142	0.6458	0.4041	11.0614	46.0354	-7.0995
6	2.0716	-0.4581	0.5293	2.3841	-0.2549	1.6736	0.3798	-0.1783	-0.781	0.2905	0.237	0.1315	0.9202	-0.4074	-0.3388	0.6077	-0.1335	-0.095	0.295	0.1774	0.476	24.9457	39.6148	-12.7576
7	3.3706	-1.5345	0.8877	2.8921	-1.1738	1.7275	0.2397	0.8614	-0.3479	-0.0186	0.0444	-0.4346	0.6484	0.2973	-0.2007	0.6122	0.1061	-0.1697	0.377	-0.1449	0.4538	31.6447	42.8826	-22.2086
8	2.4236	-0.9152	0.3567	1.4756	-0.5077	0.1796	0.3309	0.6289	-0.8943	-0.0862	0.1544	-0.3827	0.7526	0.2319	-0.2183	0.8631	0.1125	-0.2788	0.335	-0.147	0.6762	34.1124	34.5397	-18.141
9	2.7203	0.248	1.1257	1.2511	0.2059	3.1361	-0.1192	0.7582	-1.2349	-0.6694	-0.4583	0.499	0.7726	-0.6615	-0.3502	0.7067	-0.1887	-0.1288	0.6612	-0.4412	0.6926	-7.4083	57.9525	-44.8763
10	2.2122	-0.6835	-0.6488	1.7005	0.0338	2.2953	0.3466	0.6985	0.0938	-0.8165	-0.5134	0.14	-0.245	-0.6373	-0.0116	0.5128	0.1061	-0.137	0.5568	-0.0695	0.171	-2.5932	75.5403	-43.9902
11	2.8239	-0.2571	-1.0484	1.5599	-0.0903	2.6976	0.3767	0.3054	0.9513	-0.6241	-0.3462	-0.6278	-0.6159	0.1319	-0.0592	0.6199	0.0898	0.1732	0.3849	0.1963	0.519	7.3612	83.1158	-43.7371

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 189 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 190 through 340 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 341 through 536 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 32 through 117 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 118 through 172 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 173 through 340 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 341 through 423 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 424 through 536 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 32 through 140 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 141 through 340 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 341 through 536 )

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