PDB-3lwb: Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from My...

ID or keywords:

Entry

Database: PDB / ID: 3lwb

Title

Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from Mycobacterium tuberculosis

Components

D-alanine--D-alanine ligase

Keywords

LIGASE / D-alanine--D-alanine Ligase / Ddl / D-alanyl--D-alanine Ligase / Rv2981c / D-alanine /

Structural Genomics / TB Structural Genomics Consortium / TBSGC / ATP-binding / Cell shape / Cell wall biogenesis / degradation /

Magnesium /

Manganese / Metal-binding / Nucleotide-binding /

Peptidoglycan synthesis

Function / homology

Function and homology information

D-alanine-D-alanine ligase /

D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape /

ATP binding /

metal ion binding /

plasma membrane /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1 Å

Authors

Bruning, J.B. / Murillo, A.C. / Chacon, O. / Barletta, R.G. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2011
Title: Structure of the Mycobacterium tuberculosis D-Alanine:D-Alanine Ligase, a Target of the Antituberculosis Drug D-Cycloserine.
Authors: Bruning, J.B. / Murillo, A.C. / Chacon, O. / Barletta, R.G. / Sacchettini, J.C.

History

Deposition	Feb 23, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lwb.cif.gz	249.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3lwb.ent.gz	198.7 KB	Display	PDB format
PDBx/mmJSON format	3lwb.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/lw/3lwb ftp://data.pdbj.org/pub/pdb/validation_reports/lw/3lwb	HTTPS FTP

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Related structure data

Related structure data	2i87S S: Starting model for refinement
Similar structure data	2va6-1 2va5-1 4hg2-d 3c94-d 6nfz-d 2bbs-d 3phg-d 2iuy-d 4y9u-2 6nq4-d 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: Rv2981c

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#192 - Dec 2015 Vancomycin similarity (13) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (12) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (3)

Deposited unit

A: D-alanine--D-alanine ligase

B: D-alanine--D-alanine ligase

hetero molecules

79.6 kDa, 2 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)	51.720, 108.302, 69.064
Angle α, β, γ (deg.)	90.000, 99.920, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	D-alanine--D-alanine ligase / D-alanylalanine synthetase / D-Ala-D-Ala ligase Mass: 39754.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Gateway MBP fusion clone / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ddl, ddlA, MT3059, MTCY349.06, Rv2981c / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P95114, UniProt: P9WP31*PLUS, D-alanine-D-alanine ligase
#2: Chemical	ChemComp-NO3 / NITRATE ION / Nitrate Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.4 Å³/Da / Density % sol: 48.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Well solution consisted of 20% PEG 3350, 0.1M potassium nitrate. 1uL of well solution was mixed with 1uL protein solution (10mg/mL) and equilibrated over 500uL well solution., pH 8, VAPOR ...Details: Well solution consisted of 20% PEG 3350, 0.1M potassium nitrate. 1uL of well solution was mixed with 1uL protein solution (10mg/mL) and equilibrated over 500uL well solution., pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 2.4 Å³/Da / Density % sol: 48.67 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Well solution consisted of 20% PEG 3350, 0.1M potassium nitrate. 1uL of well solution was mixed with 1uL protein solution (10mg/mL) and equilibrated over 500uL well solution., pH 8, VAPOR ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.96411 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2004 / Details: mirrors
Radiation	Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96411 Å / Relative weight: 1
Reflection	Resolution: 2.1→20 Å / Num. all: 40957 / Num. obs: 40957 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / B_iso Wilson estimate: 34.16 Å² / R_merge(I) obs: 0.052 / R_sym value: 0.052 / Χ²: 1.162 / Net I/σ(I): 10.5
Reflection shell	Resolution: 2.1→2.17 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.406 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3686 / R_sym value: 0.406 / Χ²: 1.106 / % possible all: 84.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: homology model derived from PDB ENTRY 2I87

2i87

Resolution: 2.1→19.203 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.834 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.221	1896	4.89 %	random
R_work	0.173	-	-	-
all	-	38758	-	-
obs	-	38758	88.75 %	-

Solvent computation

B_sol: 66.984 Å² / k_sol: 0.329 e/Å³

Displacement parameters

B_iso max: 151.9 Å² / B_iso mean: 45.294 Å² / B_iso min: 16.2 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.401 Å²	-0 Å²	-0.404 Å²
2-	-	0.82 Å²	-0 Å²
3-	-	-	-0.42 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→19.203 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4510	0	8	383	4901

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.622	1
X-RAY DIFFRACTION	f_bond_d	0.004	1
X-RAY DIFFRACTION	f_chiral_restr	0.046	1
X-RAY DIFFRACTION	f_dihedral_angle_d	9.793	1
X-RAY DIFFRACTION	f_plane_restr	0.002	1
X-RAY DIFFRACTION	f_nbd_refined	4.063	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Num. reflection obs	Total num. of bins used	% reflection obs (%)
2.1-2.109	0.291	335	X-RAY DIFFRACTION	335	74	57
2.109-2.119	0.302	373	X-RAY DIFFRACTION	373	74	65
2.119-2.129	0.269	415	X-RAY DIFFRACTION	415	74	69
2.129-2.139	0.266	423	X-RAY DIFFRACTION	423	74	73
2.139-2.149	0.269	424	X-RAY DIFFRACTION	424	74	70
2.149-2.16	0.25	415	X-RAY DIFFRACTION	415	74	70
2.16-2.171	0.259	411	X-RAY DIFFRACTION	411	74	72
2.171-2.181	0.247	427	X-RAY DIFFRACTION	427	74	73
2.181-2.193	0.245	420	X-RAY DIFFRACTION	420	74	74
2.193-2.204	0.235	465	X-RAY DIFFRACTION	465	74	77
2.204-2.215	0.224	426	X-RAY DIFFRACTION	426	74	76
2.215-2.227	0.22	472	X-RAY DIFFRACTION	472	74	75
2.227-2.239	0.222	390	X-RAY DIFFRACTION	390	74	69
2.239-2.252	0.231	452	X-RAY DIFFRACTION	452	74	75
2.252-2.264	0.225	476	X-RAY DIFFRACTION	476	74	81
2.264-2.277	0.2	431	X-RAY DIFFRACTION	431	74	77
2.277-2.29	0.195	440	X-RAY DIFFRACTION	440	74	76
2.29-2.304	0.206	476	X-RAY DIFFRACTION	476	74	78
2.304-2.318	0.19	447	X-RAY DIFFRACTION	447	74	76
2.318-2.332	0.19	457	X-RAY DIFFRACTION	457	74	80
2.332-2.346	0.177	456	X-RAY DIFFRACTION	456	74	76
2.346-2.362	0.17	463	X-RAY DIFFRACTION	463	74	79
2.362-2.377	0.171	491	X-RAY DIFFRACTION	491	74	81
2.377-2.392	0.178	459	X-RAY DIFFRACTION	459	74	80
2.392-2.409	0.172	454	X-RAY DIFFRACTION	454	74	81
2.409-2.425	0.158	476	X-RAY DIFFRACTION	476	74	80
2.425-2.442	0.175	468	X-RAY DIFFRACTION	468	74	80
2.442-2.46	0.18	500	X-RAY DIFFRACTION	500	74	79
2.46-2.478	0.165	470	X-RAY DIFFRACTION	470	74	82
2.478-2.496	0.17	483	X-RAY DIFFRACTION	483	74	85
2.496-2.516	0.159	483	X-RAY DIFFRACTION	483	74	83
2.516-2.535	0.168	486	X-RAY DIFFRACTION	486	74	82
2.535-2.556	0.19	492	X-RAY DIFFRACTION	492	74	83
2.556-2.577	0.185	487	X-RAY DIFFRACTION	487	74	82
2.577-2.599	0.186	508	X-RAY DIFFRACTION	508	74	86
2.599-2.621	0.174	507	X-RAY DIFFRACTION	507	74	86
2.621-2.645	0.167	473	X-RAY DIFFRACTION	473	74	84
2.645-2.669	0.186	532	X-RAY DIFFRACTION	532	74	87
2.669-2.694	0.188	491	X-RAY DIFFRACTION	491	74	85
2.694-2.72	0.176	521	X-RAY DIFFRACTION	521	74	84
2.72-2.747	0.174	512	X-RAY DIFFRACTION	512	74	89
2.747-2.775	0.179	517	X-RAY DIFFRACTION	517	74	88
2.775-2.805	0.202	507	X-RAY DIFFRACTION	507	74	88
2.805-2.835	0.188	519	X-RAY DIFFRACTION	519	74	88
2.835-2.868	0.186	526	X-RAY DIFFRACTION	526	74	87
2.868-2.901	0.175	511	X-RAY DIFFRACTION	511	74	90
2.901-2.936	0.165	527	X-RAY DIFFRACTION	527	74	89
2.936-2.973	0.186	524	X-RAY DIFFRACTION	524	74	90
2.973-3.012	0.183	553	X-RAY DIFFRACTION	553	74	91
3.012-3.053	0.191	548	X-RAY DIFFRACTION	548	74	91
3.053-3.097	0.179	535	X-RAY DIFFRACTION	535	74	93
3.097-3.143	0.171	536	X-RAY DIFFRACTION	536	74	91
3.143-3.192	0.167	561	X-RAY DIFFRACTION	561	74	94
3.192-3.244	0.183	551	X-RAY DIFFRACTION	551	74	93
3.244-3.3	0.183	530	X-RAY DIFFRACTION	530	74	93
3.3-3.359	0.167	552	X-RAY DIFFRACTION	552	74	93
3.359-3.424	0.166	565	X-RAY DIFFRACTION	565	74	92
3.424-3.493	0.164	530	X-RAY DIFFRACTION	530	74	94
3.493-3.569	0.148	567	X-RAY DIFFRACTION	567	74	94
3.569-3.651	0.166	568	X-RAY DIFFRACTION	568	74	94
3.651-3.742	0.161	549	X-RAY DIFFRACTION	549	74	94
3.742-3.842	0.152	546	X-RAY DIFFRACTION	546	74	94
3.842-3.954	0.142	556	X-RAY DIFFRACTION	556	74	93
3.954-4.081	0.149	559	X-RAY DIFFRACTION	559	74	94
4.081-4.225	0.147	550	X-RAY DIFFRACTION	550	74	94
4.225-4.392	0.144	566	X-RAY DIFFRACTION	566	74	94
4.392-4.589	0.129	565	X-RAY DIFFRACTION	565	74	94
4.589-4.828	0.132	540	X-RAY DIFFRACTION	540	74	94
4.828-5.125	0.145	581	X-RAY DIFFRACTION	581	74	95
5.125-5.512	0.167	550	X-RAY DIFFRACTION	550	74	95
5.512-6.051	0.19	566	X-RAY DIFFRACTION	566	74	95
6.051-6.891	0.182	566	X-RAY DIFFRACTION	566	74	94
6.891-8.552	0.154	585	X-RAY DIFFRACTION	585	74	95
8.552-19.204	0.17	569	X-RAY DIFFRACTION	569	74	93

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	0.8244	0.187	0.0426	0.8305	-0.1246	0.4929	-0.0357	-0.0533	0.226	0.1454	0.0107	0.1164	-0.1717	-0.0181	0.0258	0.1148	0.0085	0.0032	0.0563	-0.0015	0.1175	19.1404	12.0113	1.9266
2	0.7541	-0.1292	0.483	0.5992	-0.7162	1.0906	0.0409	0.0518	-0.0571	-0.0579	-0.0297	0.008	0.201	0.0277	-0.0099	0.1252	-0.0032	0.0066	0.035	-0.0172	0.1094	16.1267	-3.0499	-2.4732
3	2.7205	0.0973	-2.4217	0.6435	-0.3755	1.4012	0.5905	-0.1627	0.4739	-0.3491	0.1334	-0.0767	-0.6788	0.4941	-0.4717	0.7596	-0.0817	0.1832	0.702	-0.1233	0.5283	18.1185	20.5808	33.6831
4	1.1168	0.0291	0.2416	0.4999	0.0677	2.443	-0.0058	-0.0947	0.0452	0.0461	0.0493	0.012	0.1143	0.203	-0.0403	0.0968	0.0526	0.0147	0.1513	-0.0101	0.1029	-0.6611	6.436	25.1753

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 7:187)	A	7 - 187
2	X-RAY DIFFRACTION	2	(chain A and resid 188:368)	A	188 - 368
3	X-RAY DIFFRACTION	3	(chain B and resid 10:129)	B	10 - 129
4	X-RAY DIFFRACTION	4	(chain B and resid 130:373)	B	130 - 373

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