PDB-5crf: Structure of the penicillin-binding protein PonA1 from Mycobacter...

ID or keywords:

Entry

Database: PDB / ID: 5crf

Title

Structure of the penicillin-binding protein PonA1 from Mycobacterium Tuberculosis

Components

Penicillin-binding protein 1A

Keywords

PENICILLIN-BINDING PROTEIN / b-lactam / PBP / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI

Function / homology

Function and homology information

peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / cellular response to hypoxia ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Kieser, K. / Endres, M. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Citation

Journal: Febs J. / Year: 2016
Title: Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance.
Authors: Filippova, E.V. / Kieser, K.J. / Luan, C.H. / Wawrzak, Z. / Kiryukhina, O. / Rubin, E.J. / Anderson, W.F.

History

Deposition	Jul 22, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 6, 2016	Group: Database references
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5crf.cif.gz	587.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5crf.ent.gz	484.6 KB	Display	PDB format
PDBx/mmJSON format	5crf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5crf_validation.pdf.gz	469.3 KB	Display	wwPDB validaton report
Full document	5crf_full_validation.pdf.gz	480 KB	Display
Data in XML	5crf_validation.xml.gz	62 KB	Display
Data in CIF	5crf_validation.cif.gz	91 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cr/5crf ftp://data.pdbj.org/pub/pdb/validation_reports/cr/5crf	HTTPS FTP

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Related structure data

Related structure data	5cxwC C: citing same article (ref.)
Similar structure data	3b9z-d 3b9y-d 2ncd-d 4jd1-d 5d88-1 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) 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-apc105958

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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: Penicillin-binding protein 1A

B: Penicillin-binding protein 1A

C: Penicillin-binding protein 1A

D: Penicillin-binding protein 1A

hetero molecules

179 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Penicillin-binding protein 1A

hetero molecules

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

2

B: Penicillin-binding protein 1A

hetero molecules

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

3

C: Penicillin-binding protein 1A

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

4

D: Penicillin-binding protein 1A

hetero molecules

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

5

Idetical with deposited unit
defined by software

6

A: Penicillin-binding protein 1A

D: Penicillin-binding protein 1A

hetero molecules

B: Penicillin-binding protein 1A

C: Penicillin-binding protein 1A

hetero molecules

defined by software
179 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.006, 333.314, 47.528
Angle α, β, γ (deg.)	90.00, 108.37, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Penicillin-binding protein 1A / PBP-1A / Penicillin-binding protein 1* Mass: 44637.605 Da / Num. of mol.: 4 / Fragment: UNP residues 391-820 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ponA1, Rv0050, MTCY21D4.13 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: P71707
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	The protein degraded during crystallization experiments. The C-terminal transpeptidase domain was ...The protein degraded during crystallization experiments. The C-terminal transpeptidase domain was crystallized and obtained in the crystal structure.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.81 Å³/Da / Density % sol: 31.91 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Lithium chloride, 0.1 M HEPES, 20 % PEG6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987857 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2014
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987857 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 120754 / % possible obs: 96.8 % / Redundancy: 4.9 % / R_merge(I) obs: 0.07 / Net I/σ(I): 30.3
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 2.4 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0103	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→30 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.955 / SU B: 6.084 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20523	6020	5 %	RANDOM
R_work	0.16083	-	-	-
obs	0.16302	114638	96.58 %	-

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: 31.899 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4 Å²	0 Å²	-0.62 Å²
2-	-	-1.48 Å²	0 Å²
3-	-	-	0.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11194	0	25	962	12181

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	11501
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10727
X-RAY DIFFRACTION	r_angle_refined_deg	1.645	1.965	15684
X-RAY DIFFRACTION	r_angle_other_deg	0.989	3	24714
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.042	5	1536
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.51	25.474	464
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.274	15	1614
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.423	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1779
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	13468
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2477
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.012	1.626	6165
X-RAY DIFFRACTION	r_mcbond_other	1.011	1.626	6164
X-RAY DIFFRACTION	r_mcangle_it	1.731	2.425	7694
X-RAY DIFFRACTION	r_mcangle_other	1.731	2.426	7695
X-RAY DIFFRACTION	r_scbond_it	1.215	1.792	5336
X-RAY DIFFRACTION	r_scbond_other	1.197	1.781	5317
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.962	2.62	7961
X-RAY DIFFRACTION	r_long_range_B_refined	6.232	14.325	13384
X-RAY DIFFRACTION	r_long_range_B_other	6.091	13.657	12976
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.799→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.272	460	-
R_work	0.236	8444	-
obs	-	-	95.55 %

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	1.7893	-1.4468	2.1552	6.2357	-5.1208	6.187	0.1871	0.0028	0.0168	-0.3092	-0.1884	-0.387	0.0302	0.3504	0.0013	0.1163	-0.0026	0.0941	0.1376	-0.0112	0.1073	15.1956	222.6907	25.553
2	0.3236	0.1646	0.2472	3.1884	0.0933	0.73	0.0197	0.0428	-0.0425	0.0192	0.0161	-0.1296	0.1093	0.0781	-0.0358	0.0724	0.0157	0.0557	0.1825	0.0081	0.0743	11.3293	243.8989	24.3635
3	0.3607	0.6196	0.0597	3.6115	0.159	0.3265	0.0398	-0.0317	-0.0629	0.4338	-0.0139	-0.2339	0.0182	0.0276	-0.0259	0.0982	0.0134	0.0066	0.1528	0.0193	0.0426	14.1005	247.0305	33.9
4	0.4927	0.149	0.0183	2.9809	0.4178	1.4875	-0.0287	0.0441	-0.0195	0.0227	0.0009	0.1626	-0.0024	-0.0281	0.0278	0.0367	0.0041	0.0511	0.1728	0.0161	0.0778	6.2536	250.6216	24.6266
5	1.3074	-2.6367	0.4948	7.2403	-0.9908	0.1948	-0.0201	-0.0168	-0.0106	0.1023	0.0019	0.3157	0.0156	0.0146	0.0182	0.1756	0.0655	0.031	0.0888	0.0218	0.1581	-12.1119	291.9713	28.3274
6	1.8843	-1.3291	-0.1075	2.1301	0.8572	0.7586	0.0096	0.142	0.2766	-0.0672	0.0074	-0.1575	-0.1211	0.0894	-0.0169	0.0474	-0.0308	0.0357	0.1095	0.0528	0.1383	-6.7274	222.7188	5.3833
7	1.8673	0.3851	0.241	1.4955	0.1872	1.5439	0.0741	0.1832	0.1774	-0.0067	0.0231	-0.0263	-0.1297	0.0752	-0.0972	0.0277	-0.0051	0.0362	0.1285	0.0296	0.0962	-8.133	213.4503	3.8933
8	0.9157	0.1352	0.3146	0.6992	0.0698	0.3241	0.1193	0.1117	-0.0513	-0.0117	0.0004	0.0741	0.1595	-0.0312	-0.1198	0.1223	-0.0269	-0.024	0.1533	0.0034	0.1148	-18.47	199.473	4.1773
9	1.2399	0.584	0.0724	0.8405	-0.0292	0.4647	0.1333	0.0539	-0.1267	0.1202	-0.0379	-0.0736	0.1075	0.0357	-0.0954	0.0779	0.001	-0.0132	0.1185	-0.0025	0.089	-7.0153	200.679	9.1306
10	0.4009	1.891	-0.7278	9.0653	-3.5444	1.4373	-0.0573	0.0386	-0.005	-0.0509	0.1637	-0.0294	-0.0489	-0.0867	-0.1064	0.2484	0.0157	-0.0216	0.1009	0.0636	0.4177	-14.0954	160.0807	26.1301
11	8.1734	-4.5618	-0.6691	7.5724	1.4163	7.0944	0.072	0.1559	-0.3689	-0.0779	-0.2361	-0.0377	0.2631	0.4732	0.1641	0.0579	-0.0056	-0.0452	0.0651	0.0419	0.3564	7.1315	139.0214	12.7969
12	1.2413	-0.2458	-0.4423	1.2376	-0.9955	1.1779	-0.0443	0.0918	-0.2326	0.0362	-0.0654	0.0235	0.0193	-0.0526	0.1097	0.0968	-0.0596	-0.1308	0.1097	-0.0326	0.38	-2.7506	150.9362	14.3796
13	1.1167	-0.3571	-0.4402	3.046	0.1594	0.6416	0.2013	0.0992	-0.1087	-0.1284	-0.132	0.0734	-0.0859	-0.0715	-0.0693	0.1195	-0.0189	-0.1268	0.1049	-0.01	0.2286	11.2668	175.3284	10.5364
14	1.099	0.3232	-0.3152	0.6346	-0.0758	0.0936	0.0748	0.0036	-0.192	0.0866	-0.1006	-0.043	-0.0118	0.0019	0.0258	0.0953	-0.0383	-0.1502	0.0789	-0.0014	0.3022	3.7805	160.8373	16.1003
15	0.3688	-1.251	0.1666	8.5151	-0.5431	0.44	0.1958	0.0429	-0.0753	-0.1981	-0.2024	0.1191	0.0149	0.0244	0.0067	0.193	-0.0436	-0.0356	0.1263	-0.0371	0.0908	10.0245	194.0865	25.3595
16	1.1644	0.5307	-0.6916	4.0858	-2.4279	1.59	0.0871	0.0145	0.0659	0.1823	-0.1593	-0.0545	-0.1401	0.085	0.0721	0.0836	0.0045	-0.0514	0.0865	-0.0118	0.1963	1.4495	308.9243	13.3104
17	0.7867	-0.1003	0.1756	3.7297	-0.1833	2.1815	-0.121	-0.0449	0.1966	0.013	-0.1195	-0.1415	-0.2109	0.1176	0.2404	0.0603	-0.0123	-0.0124	0.0867	0.0198	0.126	3.6556	292.2908	18.595
18	6.5089	-1.4839	0.3613	2.833	0.3092	0.9088	0.0677	-0.3274	-0.2041	-0.5966	-0.0243	-0.1889	-0.0552	0.1204	-0.0434	0.1552	0.0378	0.0563	0.0971	0.021	0.0294	7.3416	268.8263	4.8707
19	0.4779	-0.448	0.2702	4.0213	-0.0555	0.4988	0.03	0.1123	0.1329	-0.7426	-0.1289	-0.2186	-0.0339	0.1297	0.0989	0.1887	0.0177	0.0638	0.1158	0.0566	0.0757	5.457	286.66	4.1147
20	0.571	-0.1626	0.3975	3.2937	-0.2506	2.1738	-0.0158	0.0347	0.1464	-0.405	-0.1597	0.1287	-0.0296	0.0937	0.1755	0.0774	0.0236	0.0129	0.0985	0.0157	0.1145	-0.4491	283.5138	12.9252
21	0.4392	0.1508	0.1114	3.1356	0.3227	0.103	-0.0489	-0.0747	0.0606	-0.1088	-0.0881	0.5165	-0.0006	-0.0349	0.1371	0.0444	0.0147	0.017	0.1364	-0.0106	0.2036	-5.8784	274.992	15.1818

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	249 - 275
2	X-RAY DIFFRACTION	2	A	276 - 376
3	X-RAY DIFFRACTION	3	A	377 - 497
4	X-RAY DIFFRACTION	4	A	498 - 624
5	X-RAY DIFFRACTION	5	A	625 - 643
6	X-RAY DIFFRACTION	6	B	253 - 309
7	X-RAY DIFFRACTION	7	B	310 - 345
8	X-RAY DIFFRACTION	8	B	346 - 495
9	X-RAY DIFFRACTION	9	B	496 - 624
10	X-RAY DIFFRACTION	10	B	625 - 643
11	X-RAY DIFFRACTION	11	C	250 - 275
12	X-RAY DIFFRACTION	12	C	276 - 346
13	X-RAY DIFFRACTION	13	C	347 - 434
14	X-RAY DIFFRACTION	14	C	435 - 613
15	X-RAY DIFFRACTION	15	C	614 - 643
16	X-RAY DIFFRACTION	16	D	250 - 295
17	X-RAY DIFFRACTION	17	D	296 - 350
18	X-RAY DIFFRACTION	18	D	351 - 385
19	X-RAY DIFFRACTION	19	D	386 - 494
20	X-RAY DIFFRACTION	20	D	495 - 576
21	X-RAY DIFFRACTION	21	D	577 - 643

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