PDB-3mfd: The Structure of the Beta-lactamase superfamily domain of D-alany...

ID or keywords:

Entry

Database: PDB / ID: 3mfd

Title

The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis

Components

D-alanyl-D-alanine carboxypeptidase dacB

Keywords

HYDROLASE / penicillin-binding protein 5* /

Beta-lactamase /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

serine-type D-Ala-D-Ala carboxypeptidase /

serine-type D-Ala-D-Ala carboxypeptidase activity / sporulation resulting in formation of a cellular spore / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape /

endopeptidase activity /

membrane
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.75 Å

Authors

Cuff, M.E. / Rakowski, E. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis.
Authors: Cuff, M.E. / Rakowski, E. / Buck, K. / Joachimiak, A.

History

Deposition	Apr 1, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3mfd.cif.gz	161.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3mfd.ent.gz	131.6 KB	Display	PDB format
PDBx/mmJSON format	3mfd.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/mf/3mfd ftp://data.pdbj.org/pub/pdb/validation_reports/mf/3mfd	HTTPS FTP

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Related structure data

Similar structure data	6cmq-1 6om4-2 5dtu-d 5la0-d 6bmb-d 3azv-1 4gmd-1 5z9e-d 2gpt-d 4l51-d 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	TargetDB: APC37676.1

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Links

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

Deposited unit

A: D-alanyl-D-alanine carboxypeptidase dacB

B: D-alanyl-D-alanine carboxypeptidase dacB

hetero molecules

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

1

A: D-alanyl-D-alanine carboxypeptidase dacB

hetero molecules

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

2

B: D-alanyl-D-alanine carboxypeptidase dacB

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.439, 100.439, 171.853
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	D-alanyl-D-alanine carboxypeptidase dacB / DD-carboxypeptidase / DD-peptidase / Penicillin-binding protein 5* / PBP-5* Mass: 38350.812 Da / Num. of mol.: 2 / Fragment: Beta-lactamase domain residues 27-358 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU23190, dacB, DacC / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P35150, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.46 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M ammonium citrate tribasic pH 7.0, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97948, 0.97923

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 12, 2009

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97948	1
2	0.97923	1

Reflection

Redundancy: 15.3 % / Av σ(I) over netI: 35.59 / Number: 1341390 / R_merge(I) obs: 0.107 / Χ²: 1.9 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 87904 / % possible obs: 98.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.75	50	96.8	1	0.085	5.661	14.7
3.77	4.75	99.4	1	0.072	3.513	15.4
3.29	3.77	99.6	1	0.075	3.022	15.7
2.99	3.29	99.9	1	0.093	2.985	16
2.78	2.99	99.9	1	0.106	2.608	16.1
2.61	2.78	100	1	0.122	2.328	16.2
2.48	2.61	100	1	0.128	1.902	16.3
2.38	2.48	100	1	0.143	1.703	16.3
2.28	2.38	100	1	0.16	1.49	16.3
2.2	2.28	100	1	0.175	1.345	16.3
2.14	2.2	100	1	0.187	1.219	16.3
2.07	2.14	100	1	0.221	1.17	16.3
2.02	2.07	100	1	0.256	1.102	16.2
1.97	2.02	100	1	0.311	1.028	16.2
1.93	1.97	100	1	0.394	0.989	16.1
1.89	1.93	100	1	0.477	1.001	15.7
1.85	1.89	100	1	0.599	0.97	14.1
1.81	1.85	98.2	1	0.677	0.978	12.4
1.78	1.81	92	1	0.794	0.977	11.2
1.75	1.78	85.3	1	0.884	0.983	10.4

Reflection

Resolution: 1.75→50 Å / Num. all: 87904 / Num. obs: 87904 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 15.3 % / R_merge(I) obs: 0.107 / Net I/σ(I): 9.3

Reflection shell

Resolution: 1.75→1.78 Å / Redundancy: 10.4 % / R_merge(I) obs: 0.884 / % possible all: 85.3

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.75 Å / D res low: 50 Å / FOM : 0.476 / FOM acentric: 0.494 / FOM centric: 0.302 / Reflection: 86837 / Reflection acentric: 78511 / Reflection centric: 8326

Phasing MAD set

Highest resolution: 1.75 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.8	1	0.8	0.5	0	0	78511	8326
2	0.9	0.85	21.8	30.6	0.77	0.63	62097	7203

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	11.24-50	1.51	1	1.8	1	0	0	208	132
1	6.33-11.24	1.35	1	1.6	1.1	0	0	1243	416
1	4.41-6.33	1.31	1	1.5	1	0	0	3144	673
1	3.38-4.41	1.08	1	1.2	1.1	0	0	5942	915
1	2.74-3.38	1.56	1	1	0.6	0	0	9565	1204
1	2.31-2.74	2.15	1	0.9	0.4	0	0	14046	1465
1	1.99-2.31	2.14	1	0.6	0.3	0	0	19501	1723
1	1.75-1.99	3.07	1	0.5	0.2	0	0	24862	1798
2	11.24-50	0.86	0.92	42.4	47.8	1.09	0.82	208	131
2	6.33-11.24	0.82	0.82	34.6	40.8	1.24	0.96	1243	416
2	4.41-6.33	0.84	0.76	32.5	37.3	1.12	0.92	3141	672
2	3.38-4.41	0.9	0.83	36	45	0.78	0.59	5934	911
2	2.74-3.38	0.89	0.84	25.9	33.8	0.81	0.62	9539	1192
2	2.31-2.74	0.9	0.84	19.1	25.4	0.81	0.6	13976	1464
2	1.99-2.31	0.94	0.92	16.9	22.9	0.63	0.44	19428	1719
2	1.75-1.99	0.96	0.96	16.3	21	0.5	0.38	8628	698

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	25.5311	-0.937	-0.552	-0.059	5.806	0
2	25.2331	-0.907	-0.518	-0.004	5.269	0
3	29.8529	-1.025	-0.5	0.032	4.896	0
4	27.3116	-0.778	-0.736	-0.13	5.075	0
5	23.9388	-0.722	-0.786	-0.175	4.765	0
6	25.2657	-1.08	-0.563	-0.039	5.091	0
7	27.5667	-0.999	-0.576	0	4.988	0
8	22.8977	-0.799	-0.71	-0.176	4.365	0
9	26.3777	-0.997	-0.521	-0.091	4.475	0
10	25.064	-0.75	-0.668	-0.174	4.055	0
11	38.1428	-0.883	-0.503	0.082	5.88	0
12	34.4126	-0.828	-0.717	-0.146	4.914	0
13	29.741	-0.789	-0.653	-0.219	3.729	0
14	32.4238	-0.741	-0.772	-0.235	3.946	0
15	26.2973	-0.922	-0.47	-0.024	3.373	0
16	43.786	-0.916	-0.616	0.123	4.002	0
17	57.1226	-0.609	-0.772	-0.233	3.83	0
18	47.0811	-0.953	-0.58	0.114	3.433	0
19	47.6493	-0.488	-0.716	-0.327	2.904	0
20	47.5528	-0.785	-0.849	-0.072	3.111	0
21	36.9163	-0.929	-0.703	0.093	3.346	0
22	45.1357	-1.074	-0.695	-0.034	2.813	0
23	27.3026	-0.962	-0.502	-0.041	2.746	0
24	49.2945	-0.588	-0.732	-0.306	3.219	0
25	29.1411	-0.793	-0.851	-0.169	3.011	0
26	45.0919	-0.986	-0.668	0.099	3.757	0
27	20.3553	-0.937	-0.552	-0.059	3.765	-0.12
28	22.5666	-0.907	-0.518	-0.004	2.995	-0.167
29	26.2856	-1.024	-0.5	0.032	2.895	-0.17
30	22.2103	-0.778	-0.736	-0.13	3.203	-0.164
31	19.1377	-0.722	-0.786	-0.175	2.908	-0.138
32	22.3602	-1.08	-0.563	-0.039	3.321	-0.181
33	22.333	-0.999	-0.576	0	2.827	-0.145
34	19.4572	-0.799	-0.71	-0.176	2.629	-0.12
35	18.5027	-0.997	-0.521	-0.091	2.526	-0.094
36	20.3046	-0.75	-0.668	-0.174	2.706	-0.075
37	35.1849	-0.883	-0.505	0.082	4.231	-0.172
38	32.762	-0.829	-0.718	-0.146	2.714	-0.121
39	23.8835	-0.788	-0.653	-0.219	2.226	-0.09
40	26.8748	-0.741	-0.772	-0.235	2.236	-0.113
41	24.7231	-0.921	-0.47	-0.024	1.738	-0.059
42	44.1361	-0.917	-0.616	0.122	2.35	-0.164
43	51.2913	-0.609	-0.772	-0.233	2.414	-0.107
44	51.5676	-0.953	-0.581	0.114	2.12	-0.079
45	37.3816	-0.488	-0.716	-0.327	1.654	-0.098
46	45.7938	-0.785	-0.849	-0.072	1.939	-0.093
47	30.5967	-0.929	-0.703	0.093	1.763	-0.075
48	38.9866	-1.074	-0.695	-0.034	1.443	-0.073
49	25.5961	-0.962	-0.502	-0.041	1.258	-0.049
50	40.9943	-0.588	-0.732	-0.306	1.965	-0.096
51	20.6107	-0.793	-0.851	-0.169	1.253	-0.079
52	47.5879	-0.985	-0.668	0.099	2.358	-0.117

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
11.24-50	0.59	0.738	0.356	340	208	132
6.33-11.24	0.683	0.765	0.44	1659	1243	416
4.41-6.33	0.692	0.741	0.464	3817	3144	673
3.38-4.41	0.637	0.674	0.393	6857	5942	915
2.74-3.38	0.644	0.675	0.396	10769	9565	1204
2.31-2.74	0.601	0.624	0.388	15511	14046	1465
1.99-2.31	0.473	0.492	0.258	21224	19501	1723
1.75-1.99	0.25	0.263	0.069	26660	24862	1798

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 86837

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.49-100	53.1	0.826	583
6.71-9.49	47.3	0.901	1099
5.48-6.71	44.6	0.901	1391
4.74-5.48	43	0.929	1624
4.24-4.74	41.8	0.938	1824
3.87-4.24	45	0.936	1994
3.59-3.87	45.3	0.932	2163
3.35-3.59	44	0.93	2317
3.16-3.35	42.3	0.922	2446
3-3.16	44.2	0.921	2580
2.86-3	44.6	0.915	2688
2.74-2.86	43.3	0.913	2817
2.63-2.74	42.9	0.916	2949
2.54-2.63	44.6	0.918	3028
2.45-2.54	43.4	0.907	3123
2.37-2.45	45	0.902	3244
2.3-2.37	47.3	0.898	3347
2.24-2.3	48.9	0.889	3424
2.18-2.24	51.1	0.894	3539
2.12-2.18	52.6	0.889	3622
2.07-2.12	52.3	0.886	3745
2.02-2.07	55.3	0.889	3806
1.98-2.02	55.8	0.882	3919
1.94-1.98	58.8	0.864	3952
1.9-1.94	61.1	0.851	4040
1.86-1.9	70	0.84	4111
1.83-1.86	70.5	0.844	4160
1.79-1.83	73.8	0.854	4093
1.75-1.79	75.8	0.82	5209

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.75→34.778 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.956 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.627 / SU ML: 0.053 / SU R Cruickshank DPI: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19014	4388	5 %	RANDOM
R_work	0.16456	-	-	-
obs	0.16583	83341	98.47 %	-
all	-	87729	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 15.672 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.91 Å²	0 Å²	0 Å²
2-	-	0.91 Å²	0 Å²
3-	-	-	-1.82 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→34.778 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4958	0	84	773	5815

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	5405
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3663
X-RAY DIFFRACTION	r_angle_refined_deg	1.393	1.972	7317
X-RAY DIFFRACTION	r_angle_other_deg	0.852	3	9028
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.075	5	694
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.947	25.064	233
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.82	15	1023
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.076	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	811
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6012
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1028
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	0.75	1.5	3281
X-RAY DIFFRACTION	r_mcbond_other	0.232	1.5	1340
X-RAY DIFFRACTION	r_mcangle_it	1.343	2	5321
X-RAY DIFFRACTION	r_scbond_it	2.41	3	2124
X-RAY DIFFRACTION	r_scangle_it	3.742	4.5	1979
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.75→1.795 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	282	-
R_work	0.275	5358	-
obs	-	-	86.32 %

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	1.0834	-0.4508	-0.5999	0.8197	0.583	3.1055	0.0791	0.026	0.0031	-0.0262	-0.1028	0.0081	0.0413	-0.1948	0.0237	0.0182	-0.0134	0.0156	0.0313	-0.0178	0.0281	-6.6324	46.5524	42.0017
2	2.9739	0.3571	-0.8068	0.677	-0.2839	0.7024	0.0301	-0.6107	0.2241	0.0424	-0.102	-0.3173	0.1052	0.424	0.0719	0.0788	0.0241	-0.0224	0.3333	-0.0216	0.2352	22.2354	49.873	57.3807
3	2.5596	-0.9204	0.5105	1.1496	-0.1004	1.4217	0.1224	0.0213	-0.0228	-0.0049	-0.0385	-0.0446	0.1437	0.0221	-0.0839	0.0829	0.041	-0.0168	0.0282	0.0086	0.0706	24.1374	27.1784	27.7941
4	0.9919	0.3195	0.0858	3.0873	-0.0044	1.1338	0.2887	0.1492	-0.5167	0.0677	-0.134	0.3974	0.6756	-0.1488	-0.1547	0.4861	-0.0265	-0.1933	0.1079	-0.0697	0.4313	7.4174	6.1629	19.5653

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-3 - 239
2	X-RAY DIFFRACTION	2	A	240 - 331
3	X-RAY DIFFRACTION	3	B	-3 - 239
4	X-RAY DIFFRACTION	4	B	240 - 331

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