PDB-3fwl: Crystal Structure of the Full-Length Transglycosylase PBP1b from ...

ID or keywords:

Entry

Database: PDB / ID: 3fwl

Title

Crystal Structure of the Full-Length Transglycosylase PBP1b from Escherichia coli

Components

Penicillin-binding protein 1B

Keywords

TRANSFERASE /

HYDROLASE / bacterial cell wall synthesis /

penicillin-binding protein / antibiotics design / Alternative initiation /

Antibiotic resistance / Cell inner membrane /

Cell membrane / Cell shape / Cell wall biogenesis/degradation /

Glycosyltransferase /

Membrane / Multifunctional enzyme /

Peptidoglycan synthesis / Signal-anchor /

Transmembrane

Function / homology

Function and homology information

positive regulation of bipolar cell growth / cell wall repair /

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 / peptidoglycan-based cell wall / outer membrane-bounded periplasmic space ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.086 Å

Authors

Sung, M.T. / Lai, Y.T. / Huang, C.Y. / Chou, L.Y. / Wong, C.H. / Ma, C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of the membrane-bound bifunctional transglycosylase PBP1b from Escherichia coli.
Authors: Sung, M.T. / Lai, Y.T. / Huang, C.Y. / Chou, L.Y. / Shih, H.W. / Cheng, W.C. / Wong, C.H. / Ma, C.

History

Deposition	Jan 19, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 2, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3fwl.cif.gz	155.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3fwl.ent.gz	126.7 KB	Display	PDB format
PDBx/mmJSON format	3fwl.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/fw/3fwl ftp://data.pdbj.org/pub/pdb/validation_reports/fw/3fwl	HTTPS FTP

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Related structure data

Related structure data	3vmaC C: citing same article (ref.)
Similar structure data	5hl9-d 4on0-d 5hla-d 5iwl-d 5xfq-d 6i2p-d 4omy-d 6ncr-d 1aer-1 2icw-2 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	#29 - May 2002 Penicillin-binding Proteins similarity (2)

Deposited unit

A: Penicillin-binding protein 1B

hetero molecules

86.4 kDa, 1 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)	63.245, 296.997, 62.824
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Penicillin-binding protein 1B / PBP-1b / PBP1b / Murein polymerase / Penicillin-insensitive transglycosylase / Peptidoglycan ...PBP-1b / PBP1b / Murein polymerase / Penicillin-insensitive transglycosylase / Peptidoglycan glycosyltransferase / Peptidoglycan TGase / Penicillin-sensitive transpeptidase / DD-transpeptidase Mass: 84866.219 Da / Num. of mol.: 1 / Fragment: residues 54-804 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0149, JW0145, mrcB, pbpF, ponB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P02919, peptidoglycan glycosyltransferase, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical	ChemComp-M0E / MOENOMYCIN / MOENOMYCIN / Moenomycin family antibiotics Mass: 1580.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆₉H₁₀₆N₅O₃₄P / Comment: antibiotic*YM

#1: Protein

Penicillin-binding protein 1B / PBP-1b / PBP1b / Murein polymerase / Penicillin-insensitive transglycosylase / Peptidoglycan ...

Mass: 84866.219 Da / Num. of mol.: 1 / Fragment: residues 54-804
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K-12 / Gene: b0149, JW0145, mrcB, pbpF, ponB / Plasmid: pET15b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P02919,

peptidoglycan glycosyltransferase,

Hydrolases; Acting on peptide bonds (peptidases)

#2: Chemical

ChemComp-M0E / MOENOMYCIN / MOENOMYCIN /

Moenomycin family antibiotics

Mass: 1580.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆₉H₁₀₆N₅O₃₄P / Comment: antibiotic*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.53 Å³/Da / Density % sol: 65.12 % / Mosaicity: 0.595 °
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20mM Tris, 300mM NaCl, 0.28mM n-Dodecyl-N,N-dimethylamine-N-oxide (LDAO), 1.2M sodium formate, 0.01M beta-Nicotinamide adenine dinucleotide hydrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: BL13B1 / Wavelength: 0.97882, 0.97899, 0.96358

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2008

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97882	1
2	0.97899	1
3	0.96358	1

Reflection

Redundancy: 8.9 % / Number: 189572 / R_merge(I) obs: 0.129 / Χ²: 1.04 / D res high: 3.15 Å / D res low: 30 Å / Num. obs: 21383 / % possible obs: 99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.76	30	95.9	1	0.084	0.977	7.6
5.38	6.76	99	1	0.11	1.044	8.8
4.7	5.38	99	1	0.096	0.964	8.6
4.27	4.7	98.3	1	0.097	0.976	8.3
3.97	4.27	99.3	1	0.12	1.079	8.9
3.73	3.97	99.9	1	0.146	1.066	9.2
3.55	3.73	100	1	0.192	1.063	9.3
3.39	3.55	100	1	0.255	1.081	9.4
3.26	3.39	100	1	0.368	1.08	9.4
3.15	3.26	100	1	0.486	1.084	9.3

Reflection

Resolution: 3.086→30 Å / Num. obs: 21677

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 3.4 Å / D res low: 30 Å / FOM : 0.53 / Reflection: 16682

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	F double prime refined	F prime refined
1	3 wavelength	1	0.9636	4.75	-3.53
1	3 wavelength	2	0.979	4.65	-11.6
1	3 wavelength	3	0.9788	7.16	-8.62

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	60	0.9	0.339	0.253	0.672
2	Se	60	0.203	0.294	0.442	0.621
3	Se	60	0.577	0.211	0.475	0.616
4	Se	60	0.235	0.104	0.256	0.538
5	Se	49.993	0.311	0.245	0.368	0.52
6	Se	60	0.956	0.342	0.259	0.595
7	Se	43.752	0.58	0.231	0.354	0.431
8	Se	60	0.324	0.28	0.439	0.684
9	Se	60	0.134	0.189	0.109	0.752
10	Se	53.464	0.855	0.27	0.39	0.581
11	Se	60	0.04	0.177	0.172	0.548
12	Se	60	0.695	0.293	0.462	0.794
13	Se	60	0.138	0.198	0.022	0.644
14	Se	60	0.879	0.198	0.404	0.611
15	Se	60	0.361	0.178	0.075	0.565
16	Se	60	0.221	0.214	0.012	0.542
17	Se	60	0.054	0.197	0.224	0.372
18	Se	60	0.467	0.053	0.265	0.47
19	Se	60	0.141	0.09	0.046	0.625
20	Se	60	0.363	0.128	0.026	0.497
21	Se	60	0.89	0.355	0.115	0.628
22	Se	40.567	0.43	0.078	0.315	0.211

Phasing MAD shell

Resolution (Å)	FOM	Reflection
11.73-30	0.49	906
7.58-11.73	0.63	1436
5.98-7.58	0.68	1791
5.09-5.98	0.63	2063
4.51-5.09	0.57	2299
4.09-4.51	0.54	2514
3.76-4.09	0.46	2777
3.51-3.76	0.35	2896

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.13	phasing
PHENIX		refinement
PDB_EXTRACT	3.006	data extraction
Blu-Ice		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 3.086→29.257 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.73 / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2733	1111	5.13 %	Random
R_work	0.2114	-	-	-
obs	0.2145	21677	95.54 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.99 Å² / k_sol: 0.312 e/Å³

Displacement parameters

B_iso max: 606.07 Å² / B_iso mean: 89.692 Å² / B_iso min: 17.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-16.4125 Å²	0 Å²	-0 Å²
2-	-	8.4676 Å²	-0 Å²
3-	-	-	-27.9232 Å²

Refinement step

Cycle: LAST / Resolution: 3.086→29.257 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5564	0	77	0	5641

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5758
X-RAY DIFFRACTION	f_angle_d	1.082	7826
X-RAY DIFFRACTION	f_dihedral_angle_d	20.166	2161
X-RAY DIFFRACTION	f_chiral_restr	0.069	889
X-RAY DIFFRACTION	f_plane_restr	0.005	1009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.086-3.2263	0.341	144	0.273	2465	94
3.2263-3.3962	0.3314	147	0.2354	2584	98
3.3962-3.6086	0.2545	127	0.2051	2616	98
3.6086-3.8867	0.2901	143	0.1932	2599	98
3.8867-4.2767	0.2381	156	0.177	2541	96
4.2767-4.8931	0.213	117	0.1617	2504	92
4.8931-6.1553	0.2552	133	0.1904	2598	96
6.1553-29.2579	0.2738	144	0.2472	2659	92

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	2.8113	0.8069	0.0756	0.3414	1.5798	0.9734	-0.3591	0.349	-0.9505	0.4598	0.1766	-0.4602	-0.6361	-0.4347	0.1988	1.9128	0.1054	0.258	0.7419	0.3193	0.6134	28.1157	138.759	25.2855
2	0.6095	-0.1744	0.0384	0.7385	-0.3752	-0.4181	0.0482	-0.7532	-0.0657	0.1544	-0.2764	0.1374	0.2378	0.0772	0.0206	0.8041	0.2374	-0.1504	1.0632	-0.1907	0.7111	37.0695	109.0434	3.5682
3	1.3289	0.092	-0.0588	0.2725	-0.1929	1.0791	-0.2664	-0.2861	0.1114	-0.1358	0.0986	0.1253	0.2685	0.1077	0.1172	0.7336	0.0146	-0.045	0.8529	0.0116	0.7655	54.2889	91.1227	6.918
4	-0.2789	-0.0897	-0.8349	1.0854	-0.6923	1.5623	-0.7213	-0.3095	0.6426	-0.3806	-0.211	0.4696	0.337	-0.2296	0.8155	0.7663	0.0072	-0.4177	0.3157	-0.1244	1.0241	39.7896	109.3514	-0.8459
5	-0.2092	0.0818	0.228	0.122	-0.1615	0.2508	0.1094	0.0275	-0.2367	-0.3641	-0.1724	-0.3402	0.9576	-0.0451	-0.0744	0.9215	0.0583	-0.2676	0.4954	-0.2031	0.7033	48.8104	124.3716	18.4122
6	0.3427	0.0152	-0.5324	0.7607	-0.3674	0.3163	0.4804	-0.1195	0.3758	0.1022	-0.0944	-0.8403	-0.5653	0.2114	-0.293	1.5586	-0.0929	-0.0604	0.6759	-0.2534	1.4185	50.4206	123.4832	9.2394
7	1.2869	-0.0343	0.4114	1.8198	0.6466	2.2011	-0.1811	0.2422	-0.014	-0.2113	0.1221	-0.0433	-0.2375	0.0389	0.0547	0.4469	0.0164	-0.0035	0.61	0.0715	0.4836	39.3973	85.9291	-24.326

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resseq 66:98)
2	X-RAY DIFFRACTION	2	chain A and (resseq 99:109)
3	X-RAY DIFFRACTION	3	chain A and (resseq 110:197)
4	X-RAY DIFFRACTION	4	chain A and (resseq 198:210)
5	X-RAY DIFFRACTION	5	chain A and (resseq 211:248)
6	X-RAY DIFFRACTION	6	chain A and (resseq 268:399)
7	X-RAY DIFFRACTION	7	chain A and (resseq 407:799)

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