PDB-5xx1: Crystal structure of Arginine decarboxylase (AdiA) from Salmonell...

ID or keywords:

Entry

Database: PDB / ID: 5xx1

Title

Crystal structure of Arginine decarboxylase (AdiA) from Salmonella typhimurium

Components

Arginine decarboxylase

Keywords

LYASE / Decamer / Phosphate bound / Salmonella typhimurium / loop movement / acid stress

Function / homology

Function and homology information

arginine decarboxylase / arginine decarboxylase activity / amino acid metabolic process / cytoplasm
Similarity search - Function

Biological species

Salmonella typhi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Deka, G. / Bharath, S.R. / Shavithri, H.S. / Murthy, M.R.N.

Funding support

India, 1items

Citation

Journal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural studies on the decameric S. typhimurium arginine decarboxylase (ADC): Pyridoxal 5'-phosphate binding induces conformational changes
Authors: Deka, G. / Bharath, S.R. / Savithri, H.S. / Murthy, M.R.N.

History

Deposition	Jun 30, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 16, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 30, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Nov 22, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	6aa9C 2vycS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vyc-2 2vyc-1 3b2u-d 5o32-d 2487 4468 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

Deposited unit

A: Arginine decarboxylase

B: Arginine decarboxylase

C: Arginine decarboxylase

D: Arginine decarboxylase

E: Arginine decarboxylase

F: Arginine decarboxylase

G: Arginine decarboxylase

H: Arginine decarboxylase

I: Arginine decarboxylase

J: Arginine decarboxylase

hetero molecules

846 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	179.360, 193.250, 280.160
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 1

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	A	A	1 - 755	1 - 755
2	1	LYS	LYS	B	B	1 - 755	1 - 755
1	2	LYS	LYS	A	A	2 - 755	2 - 755
2	2	LYS	LYS	C	C	2 - 755	2 - 755
1	3	LYS	LYS	A	A	1 - 755	1 - 755
2	3	LYS	LYS	D	D	1 - 755	1 - 755
1	4	LYS	LYS	A	A	1 - 755	1 - 755
2	4	LYS	LYS	E	E	1 - 755	1 - 755
1	5	LYS	LYS	A	A	1 - 755	1 - 755
2	5	LYS	LYS	F	F	1 - 755	1 - 755
1	6	LYS	LYS	A	A	1 - 755	1 - 755
2	6	LYS	LYS	G	G	1 - 755	1 - 755
1	7	LYS	LYS	A	A	1 - 755	1 - 755
2	7	LYS	LYS	H	H	1 - 755	1 - 755
1	8	LYS	LYS	A	A	1 - 755	1 - 755
2	8	LYS	LYS	I	I	1 - 755	1 - 755
1	9	LYS	LYS	A	A	1 - 755	1 - 755
2	9	LYS	LYS	J	J	1 - 755	1 - 755
1	10	ALA	ALA	B	B	2 - 756	2 - 756
2	10	ALA	ALA	C	C	2 - 756	2 - 756
1	11	ALA	ALA	B	B	1 - 756	1 - 756
2	11	ALA	ALA	D	D	1 - 756	1 - 756
1	12	ALA	ALA	B	B	1 - 756	1 - 756
2	12	ALA	ALA	E	E	1 - 756	1 - 756
1	13	LYS	LYS	B	B	1 - 755	1 - 755
2	13	LYS	LYS	F	F	1 - 755	1 - 755
1	14	ALA	ALA	B	B	1 - 756	1 - 756
2	14	ALA	ALA	G	G	1 - 756	1 - 756
1	15	LYS	LYS	B	B	1 - 755	1 - 755
2	15	LYS	LYS	H	H	1 - 755	1 - 755
1	16	ALA	ALA	B	B	1 - 756	1 - 756
2	16	ALA	ALA	I	I	1 - 756	1 - 756
1	17	LYS	LYS	B	B	1 - 755	1 - 755
2	17	LYS	LYS	J	J	1 - 755	1 - 755
1	18	ALA	ALA	C	C	2 - 756	2 - 756
2	18	ALA	ALA	D	D	2 - 756	2 - 756
1	19	ALA	ALA	C	C	2 - 756	2 - 756
2	19	ALA	ALA	E	E	2 - 756	2 - 756
1	20	LYS	LYS	C	C	2 - 755	2 - 755
2	20	LYS	LYS	F	F	2 - 755	2 - 755
1	21	ALA	ALA	C	C	2 - 756	2 - 756
2	21	ALA	ALA	G	G	2 - 756	2 - 756
1	22	LYS	LYS	C	C	2 - 755	2 - 755
2	22	LYS	LYS	H	H	2 - 755	2 - 755
1	23	ALA	ALA	C	C	2 - 756	2 - 756
2	23	ALA	ALA	I	I	2 - 756	2 - 756
1	24	LYS	LYS	C	C	2 - 755	2 - 755
2	24	LYS	LYS	J	J	2 - 755	2 - 755
1	25	ALA	ALA	D	D	1 - 756	1 - 756
2	25	ALA	ALA	E	E	1 - 756	1 - 756
1	26	LYS	LYS	D	D	1 - 755	1 - 755
2	26	LYS	LYS	F	F	1 - 755	1 - 755
1	27	ALA	ALA	D	D	1 - 756	1 - 756
2	27	ALA	ALA	G	G	1 - 756	1 - 756
1	28	LYS	LYS	D	D	1 - 755	1 - 755
2	28	LYS	LYS	H	H	1 - 755	1 - 755
1	29	ALA	ALA	D	D	1 - 756	1 - 756
2	29	ALA	ALA	I	I	1 - 756	1 - 756
1	30	LYS	LYS	D	D	1 - 755	1 - 755
2	30	LYS	LYS	J	J	1 - 755	1 - 755
1	31	LYS	LYS	E	E	1 - 755	1 - 755
2	31	LYS	LYS	F	F	1 - 755	1 - 755
1	32	ALA	ALA	E	E	1 - 756	1 - 756
2	32	ALA	ALA	G	G	1 - 756	1 - 756
1	33	LYS	LYS	E	E	1 - 755	1 - 755
2	33	LYS	LYS	H	H	1 - 755	1 - 755
1	34	ALA	ALA	E	E	1 - 756	1 - 756
2	34	ALA	ALA	I	I	1 - 756	1 - 756
1	35	LYS	LYS	E	E	1 - 755	1 - 755
2	35	LYS	LYS	J	J	1 - 755	1 - 755
1	36	LYS	LYS	F	F	1 - 755	1 - 755
2	36	LYS	LYS	G	G	1 - 755	1 - 755
1	37	LYS	LYS	F	F	1 - 755	1 - 755
2	37	LYS	LYS	H	H	1 - 755	1 - 755
1	38	LYS	LYS	F	F	1 - 755	1 - 755
2	38	LYS	LYS	I	I	1 - 755	1 - 755
1	39	LYS	LYS	F	F	1 - 755	1 - 755
2	39	LYS	LYS	J	J	1 - 755	1 - 755
1	40	LYS	LYS	G	G	1 - 755	1 - 755
2	40	LYS	LYS	H	H	1 - 755	1 - 755
1	41	ALA	ALA	G	G	1 - 756	1 - 756
2	41	ALA	ALA	I	I	1 - 756	1 - 756
1	42	LYS	LYS	G	G	1 - 755	1 - 755
2	42	LYS	LYS	J	J	1 - 755	1 - 755
1	43	LYS	LYS	H	H	1 - 755	1 - 755
2	43	LYS	LYS	I	I	1 - 755	1 - 755
1	44	LYS	LYS	H	H	1 - 755	1 - 755
2	44	LYS	LYS	J	J	1 - 755	1 - 755
1	45	LYS	LYS	I	I	1 - 755	1 - 755
2	45	LYS	LYS	J	J	1 - 755	1 - 755

NCS ensembles :
NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.311902, -0.006292, -0.950093), (-0.01574, 0.999807, -0.011788), (0.949984, 0.018632, 0.311743)	69.866203, 1.45267, 31.38113

#1: Protein	Arginine decarboxylase Mass: 84483.047 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: adi, t4203 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Z1P1, arginine decarboxylase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1385 / 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: 2.87 Å³/Da / Density % sol: 57.22 %
Crystal grow	Temperature: 298 K / Method: microbatch / pH: 8 / Details: 2.0M NaCl and 10% PEG8000, Tris pH 8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 17, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 3.1→57.12 Å / Num. obs: 160279 / % possible obs: 91.2 % / Redundancy: 8 % / B_iso Wilson estimate: 16.3 Å² / CC_1/2: 0.972 / R_merge(I) obs: 0.26 / R_pim(I) all: 0.095 / R_sym value: 0.278 / Net I/σ(I): 7.2
Reflection shell	Resolution: 3.1→3.27 Å / Redundancy: 7.6 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 21162 / CC_1/2: 0.799 / R_pim(I) all: 0.267 / R_sym value: 0.77 / % possible all: 83.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0069	refinement
iMOSFLM	7.1.1	data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VYC

2vyc

Resolution: 3.1→57.12 Å / Cor.coef. F_o:F_c: 0.866 / Cor.coef. F_o:F_c free: 0.826 / SU B: 23.882 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27179	7890	4.9 %	RANDOM
R_work	0.2406	-	-	-
obs	0.24213	152238	90.82 %	-

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: 28.251 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.23 Å²	0 Å²	0 Å²
2-	-	0.18 Å²	-0 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: 1 / Resolution: 3.1→57.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	56095	0	50	1385	57530

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	57564
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	52309
X-RAY DIFFRACTION	r_angle_refined_deg	0.935	1.944	78383
X-RAY DIFFRACTION	r_angle_other_deg	0.788	3	120000
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.471	5	7292
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.722	24.194	2599
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.561	15	8654
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.481	15	292
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	8601
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	66497
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	13513
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	0.543	2.915	29296
X-RAY DIFFRACTION	r_mcbond_other	0.543	2.915	29295
X-RAY DIFFRACTION	r_mcangle_it	1.005	4.37	36538
X-RAY DIFFRACTION	r_mcangle_other	1.005	4.37	36539
X-RAY DIFFRACTION	r_scbond_it	0.377	2.928	28268
X-RAY DIFFRACTION	r_scbond_other	0.375	2.923	28229
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.716	4.376	41784
X-RAY DIFFRACTION	r_long_range_B_refined	2.972	23.098	64931
X-RAY DIFFRACTION	r_long_range_B_other	2.967	23.113	64834
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	6007	TIGHT POSITIONAL	0.05	0.15
1	A	5993	TIGHT POSITIONAL	0.05	0.15
1	A	6046	TIGHT POSITIONAL	0.05	0.15
1	A	6071	TIGHT POSITIONAL	0.06	0.15
1	A	6177	TIGHT POSITIONAL	0.04	0.15
1	A	6168	TIGHT POSITIONAL	0.04	0.15
1	A	6138	TIGHT POSITIONAL	0.03	0.15
1	A	6157	TIGHT POSITIONAL	0.06	0.15
1	A	6008	TIGHT POSITIONAL	0.04	0.15
1	A	6008	TIGHT POSITIONAL	0.03	0.15
1	A	6099	TIGHT THERMAL	1.69	1.5
2	A	6019	TIGHT POSITIONAL	0.05	0.15
2	A	6118	TIGHT POSITIONAL	0.04	0.15
2	A	6116	TIGHT POSITIONAL	0.05	0.15
2	A	6100	TIGHT POSITIONAL	0.05	0.15
2	A	6130	TIGHT POSITIONAL	0.07	0.15
2	A	6056	TIGHT POSITIONAL	0.05	0.15
2	A	6079	TIGHT POSITIONAL	0.03	0.15
2	A	6152	TIGHT POSITIONAL	0.04	0.15
2	A	6166	TIGHT POSITIONAL	0.05	0.15
2	A	6136	TIGHT POSITIONAL	0.05	0.15
2	A	6074	TIGHT THERMAL	2.26	1.5
3	A	6139	TIGHT POSITIONAL	0.03	0.15
3	A	6126	TIGHT POSITIONAL	0.06	0.15
3	A	6219	TIGHT POSITIONAL	0.04	0.15
3	A	6231	TIGHT POSITIONAL	0.05	0.15
3	A	6173	TIGHT POSITIONAL	0.05	0.15
3	A	6229	TIGHT POSITIONAL	0.05	0.15
3	A	6237	TIGHT POSITIONAL	0.05	0.15
3	A	6273	TIGHT POSITIONAL	0.06	0.15
3	A	6229	TIGHT POSITIONAL	0.06	0.15
3	A	6249	TIGHT POSITIONAL	0.07	0.15
3	A	6062	TIGHT THERMAL	2.36	1.5
4	A	6408	TIGHT POSITIONAL	0.04	0.15
4	A	6352	TIGHT POSITIONAL	0.04	0.15
4	A	6373	TIGHT POSITIONAL	0.05	0.15
4	A	6371	TIGHT POSITIONAL	0.03	0.15
4	A	6405	TIGHT POSITIONAL	0.05	0.15
4	A	6316	TIGHT POSITIONAL	0.06	0.15
4	A	6111	TIGHT THERMAL	1.98	1.5
5	A	6139	TIGHT THERMAL	2.34	1.5
6	A	6248	TIGHT THERMAL	1.84	1.5
7	A	6248	TIGHT THERMAL	3.26	1.5
8	A	6221	TIGHT THERMAL	2.26	1.5
9	A	6240	TIGHT THERMAL	2.19	1.5
10	B	6007	TIGHT THERMAL	2.2	1.5
11	B	5993	TIGHT THERMAL	2.43	1.5
12	B	6046	TIGHT THERMAL	1.84	1.5
13	B	6071	TIGHT THERMAL	2.55	1.5
14	B	6177	TIGHT THERMAL	1.99	1.5
15	B	6168	TIGHT THERMAL	3.55	1.5
16	B	6138	TIGHT THERMAL	2.35	1.5
17	B	6157	TIGHT THERMAL	2	1.5
18	C	6008	TIGHT THERMAL	1.86	1.5
19	C	6008	TIGHT THERMAL	1.92	1.5
20	C	6019	TIGHT THERMAL	2.75	1.5
21	C	6118	TIGHT THERMAL	2.4	1.5
22	C	6116	TIGHT THERMAL	3.57	1.5
23	C	6100	TIGHT THERMAL	2.21	1.5
24	C	6130	TIGHT THERMAL	2.34	1.5
25	D	6056	TIGHT THERMAL	2.07	1.5
26	D	6079	TIGHT THERMAL	2.99	1.5
27	D	6152	TIGHT THERMAL	2.65	1.5
28	D	6166	TIGHT THERMAL	3.92	1.5
29	D	6136	TIGHT THERMAL	2.06	1.5
30	D	6139	TIGHT THERMAL	2.37	1.5
31	E	6126	TIGHT THERMAL	2.35	1.5
32	E	6219	TIGHT THERMAL	1.83	1.5
33	E	6231	TIGHT THERMAL	3.26	1.5
34	E	6173	TIGHT THERMAL	2.08	1.5
35	E	6229	TIGHT THERMAL	1.85	1.5
36	F	6237	TIGHT THERMAL	1.95	1.5
37	F	6273	TIGHT THERMAL	2.17	1.5
38	F	6229	TIGHT THERMAL	2.38	1.5
39	F	6249	TIGHT THERMAL	2.96	1.5
40	G	6408	TIGHT THERMAL	2.72	1.5
41	G	6352	TIGHT THERMAL	2.4	1.5
42	G	6373	TIGHT THERMAL	2.27	1.5
43	H	6371	TIGHT THERMAL	3.25	1.5
44	H	6405	TIGHT THERMAL	3.95	1.5
45	I	6316	TIGHT THERMAL	2.52	1.5

LS refinement shell

Resolution: 3.1→3.181 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.363	555	-
R_work	0.319	10168	-
obs	-	-	82.9 %

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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+About Yorodumi

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-Aug 12, 2020. Covid-19 info

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Download

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Validation report

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi