PDB-4ye5: The crystal structure of a peptidoglycan synthetase from Bifidoba...

ID or keywords:

Entry

Database: PDB / ID: 4ye5

Title

The crystal structure of a peptidoglycan synthetase from Bifidobacterium adolescentis ATCC 15703

Components

Peptidoglycan synthetase penicillin-binding protein 3

Keywords

penicillin binding protein /

structural genomics / PSI-Biology /

protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Function and homology information

penicillin binding / membrane => GO:0016020
Similarity search - Function

Biological species

Bifidobacterium adolescentis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.052 Å

Authors

Cuff, M. / Tan, K. / Joachimiak, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of a peptidoglycan synthetase from Bifidobacterium adolescentis ATCC 15703
Authors: Cuff, M. / Tan, K. / Joachimiak, G. / Clancy, S. / Joachimiak, A.

History

Deposition	Feb 23, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Source and taxonomy Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ye5.cif.gz	423.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4ye5.ent.gz	356.1 KB	Display	PDB format
PDBx/mmJSON format	4ye5.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/ye/4ye5 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4ye5	HTTPS FTP

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Related structure data

Similar structure data	6rz5-2 6eb9-1 6tsb-1 6wcw-d 4pxz-d 2gk9-2 6rz4-d 1zjk-d 3mui-d 2h03-2 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: MCSG-APC110220

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Peptidoglycan synthetase penicillin-binding protein 3

B: Peptidoglycan synthetase penicillin-binding protein 3

hetero molecules

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

1

A: Peptidoglycan synthetase penicillin-binding protein 3

hetero molecules

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

2

B: Peptidoglycan synthetase penicillin-binding protein 3

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.956, 85.709, 227.476
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Peptidoglycan synthetase penicillin-binding protein 3 Mass: 61003.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a) (bacteria) Strain: ATCC 15703 / DSM 20083 / NCTC 11814 / E194a / Gene: ftsI, BAD_1107 / Plasmid: pMCSG73 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: A1A2F5
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 555 / 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: 3.48 Å³/Da / Density % sol: 64.65 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Bis-Tris Propane:NaOH, 1.5M Ammonium Sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 102844 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / R_merge(I) obs: 0.106 / Net I/σ(I): 36.37
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 7 % / R_merge(I) obs: 0.765 / Mean I/σ(I) obs: 2.58 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.052→47.387 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2243	5101	4.96 %	Random selection
R_work	0.189	-	-	-
obs	0.1908	102844	97.22 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.052→47.387 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7944	0	34	555	8533

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8128
X-RAY DIFFRACTION	f_angle_d	1.033	11027
X-RAY DIFFRACTION	f_dihedral_angle_d	13.729	2927
X-RAY DIFFRACTION	f_chiral_restr	0.071	1283
X-RAY DIFFRACTION	f_plane_restr	0.004	1448

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 (%)
2.0522-2.0755	0.317	96	0.2346	1934	X-RAY DIFFRACTION	59
2.0755-2.0999	0.2587	121	0.2398	2505	X-RAY DIFFRACTION	75
2.0999-2.1256	0.2809	164	0.2296	3030	X-RAY DIFFRACTION	92
2.1256-2.1525	0.2721	164	0.2248	3193	X-RAY DIFFRACTION	96
2.1525-2.1808	0.2832	168	0.2193	3242	X-RAY DIFFRACTION	99
2.1808-2.2107	0.2471	184	0.2093	3346	X-RAY DIFFRACTION	100
2.2107-2.2422	0.2594	191	0.2025	3261	X-RAY DIFFRACTION	100
2.2422-2.2757	0.2358	158	0.1958	3320	X-RAY DIFFRACTION	100
2.2757-2.3113	0.2155	169	0.1947	3332	X-RAY DIFFRACTION	100
2.3113-2.3492	0.2682	168	0.1925	3285	X-RAY DIFFRACTION	100
2.3492-2.3897	0.2079	154	0.185	3387	X-RAY DIFFRACTION	100
2.3897-2.4331	0.2034	179	0.1856	3312	X-RAY DIFFRACTION	100
2.4331-2.4799	0.2233	160	0.1843	3350	X-RAY DIFFRACTION	100
2.4799-2.5305	0.2427	175	0.1813	3337	X-RAY DIFFRACTION	100
2.5305-2.5856	0.236	187	0.1929	3329	X-RAY DIFFRACTION	100
2.5856-2.6457	0.2284	180	0.1935	3272	X-RAY DIFFRACTION	100
2.6457-2.7119	0.2562	158	0.1959	3359	X-RAY DIFFRACTION	100
2.7119-2.7852	0.2353	180	0.1957	3336	X-RAY DIFFRACTION	100
2.7852-2.8671	0.2496	197	0.1898	3331	X-RAY DIFFRACTION	100
2.8671-2.9596	0.2267	185	0.1944	3351	X-RAY DIFFRACTION	100
2.9596-3.0654	0.2365	209	0.1913	3290	X-RAY DIFFRACTION	100
3.0654-3.1881	0.227	190	0.1941	3341	X-RAY DIFFRACTION	100
3.1881-3.3332	0.225	161	0.1937	3359	X-RAY DIFFRACTION	100
3.3332-3.5089	0.1997	164	0.1926	3363	X-RAY DIFFRACTION	100
3.5089-3.7286	0.2203	175	0.1829	3407	X-RAY DIFFRACTION	100
3.7286-4.0164	0.1916	181	0.1668	3363	X-RAY DIFFRACTION	100
4.0164-4.4203	0.184	176	0.1623	3394	X-RAY DIFFRACTION	100
4.4203-5.0593	0.1945	147	0.1614	3502	X-RAY DIFFRACTION	100
5.0593-6.3717	0.2085	186	0.1905	3416	X-RAY DIFFRACTION	100
6.3717-47.3994	0.239	174	0.2017	3496	X-RAY DIFFRACTION	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	0.0347	-0.3239	0.0798	2.6249	0.5585	-0.1659	-0.0422	0.014	-0.0686	0.1257	0.0043	-0.0262	0.118	0.0447	0.0312	0.3414	0.0249	0.0646	0.1466	-0.0325	0.2776	3.4451	72.4695	96.5376
2	1.4857	-0.1965	-0.4435	1.6885	0.1091	1.5814	0.0129	-0.2035	0.1609	0.2329	-0.0397	0.1593	-0.1033	-0.0175	0.034	0.1611	0.0121	0.0011	0.1064	-0.0415	0.1862	-6.5232	110.7357	111.4814
3	1.1274	-0.4957	-0.4369	0.2732	0.1825	0.1234	0.1612	0.8373	0.1348	-0.2173	-0.0291	0.3641	-0.0023	0.5543	-0.0921	0.1458	0.3417	0.2512	1.5376	0.0106	0.5702	-44.7777	114.3988	77.7437
4	1.0283	0.6198	0.5314	1.7544	0.0075	2.8277	0.0489	1.161	-0.2186	-0.3154	0.023	-0.3774	0.1574	0.0866	-0.0017	0.3371	0.0988	0.0699	0.883	-0.2071	0.2197	1.3258	100.6443	63.2473

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 55 through 333 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 334 through 600 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 55 through 254 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 255 through 600 )

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