PDB-6oyy: Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid...

ID or keywords:

Entry

Database: PDB / ID: 6oyy

Title

Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex

Components

Aspartate 1-decarboxylase alpha chain
Aspartate 1-decarboxylase beta chain

Keywords

LYASE / active /

pyrazinoic acid /

complex /

Structural Genomics / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

alanine biosynthetic process /

aspartate 1-decarboxylase /

aspartate 1-decarboxylase activity / pantothenate biosynthetic process / peptidoglycan-based cell wall /

cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Sun, Q. / Li, X. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Funding support

United States, 2items

Citation

Journal: Nat Commun / Year: 2020
Title: The molecular basis of pyrazinamide activity on Mycobacterium tuberculosis PanD.
Authors: Sun, Q. / Li, X. / Perez, L.M. / Shi, W. / Zhang, Y. / Sacchettini, J.C.

History

Deposition	May 15, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Derived calculations Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6oyy.cif.gz	147.4 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	6oyy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oy/6oyy ftp://data.pdbj.org/pub/pdb/validation_reports/oy/6oyy	HTTPS FTP

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Related structure data

Related structure data	6oz8C 6p02C 6p1yC 2c45S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6p02-1 6p02-3 6oz8-2 2c45-1 6p02-2 2c45-2 6oz8-1 1pqh-1 1pt1-1 3zu3-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#80 - Aug 2006 AAA+ Proteases similarity (1) #144 - Dec 2011 Complex I similarity (1) #167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alpha chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alpha chain

I: Aspartate 1-decarboxylase beta chain

J: Aspartate 1-decarboxylase alpha chain

E: Aspartate 1-decarboxylase beta chain

F: Aspartate 1-decarboxylase alpha chain

K: Aspartate 1-decarboxylase beta chain

L: Aspartate 1-decarboxylase alpha chain

G: Aspartate 1-decarboxylase beta chain

H: Aspartate 1-decarboxylase alpha chain

hetero molecules

96.6 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alpha chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alpha chain

hetero molecules

A: Aspartate 1-decarboxylase beta chain

B: Aspartate 1-decarboxylase alpha chain

C: Aspartate 1-decarboxylase beta chain

D: Aspartate 1-decarboxylase alpha chain

hetero molecules

defined by author&software
Evidence: gel filtration
64.4 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Aspartate 1-decarboxylase beta chain

F: Aspartate 1-decarboxylase alpha chain

G: Aspartate 1-decarboxylase beta chain

H: Aspartate 1-decarboxylase alpha chain

hetero molecules

I: Aspartate 1-decarboxylase beta chain

J: Aspartate 1-decarboxylase alpha chain

K: Aspartate 1-decarboxylase beta chain

L: Aspartate 1-decarboxylase alpha chain

hetero molecules

defined by author&software
Evidence: gel filtration
64.4 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	162.282, 162.282, 62.826
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	1	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
1	2	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	2	MET	MET	GLY	GLY	I	E	1 - 24	1 - 24
1	3	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	3	MET	MET	GLY	GLY	E	G	1 - 24	1 - 24
1	4	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	4	MET	MET	GLY	GLY	K	I	1 - 24	1 - 24
1	5	MET	MET	GLY	GLY	A	A	1 - 24	1 - 24
2	5	MET	MET	GLY	GLY	G	K	1 - 24	1 - 24
1	6	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	6	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
1	7	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	7	VAL	VAL	ILE	ILE	J	F	26 - 115	2 - 91
1	8	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	8	VAL	VAL	ILE	ILE	F	H	26 - 115	2 - 91
1	9	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	9	VAL	VAL	ILE	ILE	L	J	26 - 115	2 - 91
1	10	VAL	VAL	ILE	ILE	B	B	26 - 115	2 - 91
2	10	VAL	VAL	ILE	ILE	H	L	26 - 115	2 - 91
1	11	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	11	MET	MET	GLY	GLY	I	E	1 - 24	1 - 24
1	12	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	12	MET	MET	GLY	GLY	E	G	1 - 24	1 - 24
1	13	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	13	MET	MET	GLY	GLY	K	I	1 - 24	1 - 24
1	14	MET	MET	GLY	GLY	C	C	1 - 24	1 - 24
2	14	MET	MET	GLY	GLY	G	K	1 - 24	1 - 24
1	15	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	15	VAL	VAL	ILE	ILE	J	F	26 - 115	2 - 91
1	16	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	16	VAL	VAL	ILE	ILE	F	H	26 - 115	2 - 91
1	17	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	17	VAL	VAL	ILE	ILE	L	J	26 - 115	2 - 91
1	18	VAL	VAL	ILE	ILE	D	D	26 - 115	2 - 91
2	18	VAL	VAL	ILE	ILE	H	L	26 - 115	2 - 91
1	19	MET	MET	GLY	GLY	I	E	1 - 24	1 - 24
2	19	MET	MET	GLY	GLY	E	G	1 - 24	1 - 24
1	20	MET	MET	GLY	GLY	I	E	1 - 24	1 - 24
2	20	MET	MET	GLY	GLY	K	I	1 - 24	1 - 24
1	21	MET	MET	GLY	GLY	I	E	1 - 24	1 - 24
2	21	MET	MET	GLY	GLY	G	K	1 - 24	1 - 24
1	22	VAL	VAL	ILE	ILE	J	F	26 - 115	2 - 91
2	22	VAL	VAL	ILE	ILE	F	H	26 - 115	2 - 91
1	23	VAL	VAL	ILE	ILE	J	F	26 - 115	2 - 91
2	23	VAL	VAL	ILE	ILE	L	J	26 - 115	2 - 91
1	24	VAL	VAL	ILE	ILE	J	F	26 - 115	2 - 91
2	24	VAL	VAL	ILE	ILE	H	L	26 - 115	2 - 91
1	25	MET	MET	GLY	GLY	E	G	1 - 24	1 - 24
2	25	MET	MET	GLY	GLY	K	I	1 - 24	1 - 24
1	26	MET	MET	GLY	GLY	E	G	1 - 24	1 - 24
2	26	MET	MET	GLY	GLY	G	K	1 - 24	1 - 24
1	27	VAL	VAL	ILE	ILE	F	H	26 - 115	2 - 91
2	27	VAL	VAL	ILE	ILE	L	J	26 - 115	2 - 91
1	28	VAL	VAL	ILE	ILE	F	H	26 - 115	2 - 91
2	28	VAL	VAL	ILE	ILE	H	L	26 - 115	2 - 91
1	29	MET	MET	GLY	GLY	K	I	1 - 24	1 - 24
2	29	MET	MET	GLY	GLY	G	K	1 - 24	1 - 24
1	30	VAL	VAL	ILE	ILE	L	J	26 - 115	2 - 91
2	30	VAL	VAL	ILE	ILE	H	L	26 - 115	2 - 91

NCS ensembles :

#1: Protein/peptide	Aspartate 1-decarboxylase beta chain Mass: 2751.341 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: panD, Rv3601c, MTCY07H7B.21 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIL3
#2: Protein	Aspartate 1-decarboxylase alpha chain Mass: 13221.777 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: panD, Rv3601c, MTCY07H7B.21 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIL3, aspartate 1-decarboxylase
#3: Chemical	ChemComp-VGL / PYRAZINE-2-CARBOXYLIC ACID / PYRAZINOIC ACID / Pyrazinoic acid Mass: 124.097 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₄N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.16 Å³/Da / Density % sol: 43.06 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, HEPES, PEG 3350, Ammonium Chloride / PH range: 6.5-7

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Data collection

Diffraction	Mean temperature: 130 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 2.7→21.92 Å / Num. obs: 23578 / % possible obs: 99.7 % / Redundancy: 15.7 % / CC_1/2: 0.999 / Net I/σ(I): 16.48
Reflection shell	Resolution: 2.7→2.796 Å / Mean I/σ(I) obs: 2.31 / Num. unique obs: 2307 / CC_1/2: 0.774 / % possible all: 99.87

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
PROTEUM PLUS		data reduction
PROTEUM PLUS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2C45

2c45

Resolution: 2.7→21.76 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.916 / SU B: 12.351 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 1.125 / ESU R Free: 0.329 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24666	1140	4.8 %	RANDOM
R_work	0.19934	-	-	-
obs	0.20159	22440	99.71 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 56.54 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.71 Å²	0 Å²	0 Å²
2-	-	-0.71 Å²	0 Å²
3-	-	-	1.41 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→21.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5262	0	0	9	5271

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	5357
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	5161
X-RAY DIFFRACTION	r_angle_refined_deg	1.437	1.657	7261
X-RAY DIFFRACTION	r_angle_other_deg	1.351	1.593	11825
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.953	5	678
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.979	20.989	263
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.601	15	871
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.916	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	753
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6053
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1109
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	4.395	5.782	2730
X-RAY DIFFRACTION	r_mcbond_other	4.393	5.781	2729
X-RAY DIFFRACTION	r_mcangle_it	6.456	8.651	3393
X-RAY DIFFRACTION	r_mcangle_other	6.455	8.652	3394
X-RAY DIFFRACTION	r_scbond_it	5.006	6.415	2626
X-RAY DIFFRACTION	r_scbond_other	5.006	6.416	2627
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	7.469	9.434	3865
X-RAY DIFFRACTION	r_long_range_B_refined	9.155		10197
X-RAY DIFFRACTION	r_long_range_B_other	9.155		10196
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	514	0.05
1	2	C	514	0.05
2	1	A	515	0.07
2	2	I	515	0.07
3	1	A	503	0.12
3	2	E	503	0.12
4	1	A	516	0.09
4	2	K	516	0.09
5	1	A	501	0.1
5	2	G	501	0.1
6	1	B	2554	0.05
6	2	D	2554	0.05
7	1	B	2540	0.07
7	2	J	2540	0.07
8	1	B	2565	0.06
8	2	F	2565	0.06
9	1	B	2542	0.06
9	2	L	2542	0.06
10	1	B	2532	0.08
10	2	H	2532	0.08
11	1	C	522	0.06
11	2	I	522	0.06
12	1	C	510	0.11
12	2	E	510	0.11
13	1	C	524	0.08
13	2	K	524	0.08
14	1	C	511	0.08
14	2	G	511	0.08
15	1	D	2548	0.05
15	2	J	2548	0.05
16	1	D	2550	0.07
16	2	F	2550	0.07
17	1	D	2565	0.05
17	2	L	2565	0.05
18	1	D	2542	0.06
18	2	H	2542	0.06
19	1	I	513	0.12
19	2	E	513	0.12
20	1	I	522	0.09
20	2	K	522	0.09
21	1	I	507	0.1
21	2	G	507	0.1
22	1	J	2577	0.06
22	2	F	2577	0.06
23	1	J	2576	0.05
23	2	L	2576	0.05
24	1	J	2562	0.07
24	2	H	2562	0.07
25	1	E	512	0.09
25	2	K	512	0.09
26	1	E	510	0.09
26	2	G	510	0.09
27	1	F	2542	0.07
27	2	L	2542	0.07
28	1	F	2546	0.07
28	2	H	2546	0.07
29	1	K	510	0.1
29	2	G	510	0.1
30	1	L	2534	0.06
30	2	H	2534	0.06

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.359	80	-
R_work	0.332	1627	-
obs	-	-	99.82 %

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