PDB-2x3l: Crystal Structure of the Orn_Lys_Arg decarboxylase family protein...

ID or keywords:

Entry

Database: PDB / ID: 2x3l

Title

Crystal Structure of the Orn_Lys_Arg decarboxylase family protein SAR0482 from Methicillin-resistant Staphylococcus aureus

Components

ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN

Keywords

LYASE

Function / homology

Function and homology information

carboxy-lyase activity
Similarity search - Function

Biological species

STAPHYLOCOCCUS AUREUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.

Citation

Journal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...

History

Deposition	Jan 25, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2	Apr 9, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _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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Validation report

Summary document	2x3l_validation.pdf.gz	462.4 KB	Display	wwPDB validaton report
Full document	2x3l_full_validation.pdf.gz	471.3 KB	Display
Data in XML	2x3l_validation.xml.gz	35.4 KB	Display
Data in CIF	2x3l_validation.cif.gz	47 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3l ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3l	HTTPS FTP

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Related structure data

Related structure data	2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C C: citing same article (ref.)
Similar structure data	4kx7-d 4rit-d 4e6y-2 5lg6-2 4xmt-d 2yd0-d 4fys-d 6m8p-18 6m8p-8 6eed-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (1)

Deposited unit

A: ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN

B: ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN

hetero molecules

104 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)	50.677, 137.283, 62.258
Angle α, β, γ (deg.)	90.00, 109.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B

NCS domain segments:

Component-ID: 1 / Refine code: 4

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	PRO	PRO	LEU	LEU	A	A	5 - 139	5 - 139
2	1	PRO	PRO	LEU	LEU	B	B	5 - 139	5 - 139
1	2	HIS	HIS	SER	SER	A	A	147 - 358	147 - 358
2	2	HIS	HIS	SER	SER	B	B	147 - 358	147 - 358
1	3	TRP	TRP	VAL	VAL	A	A	384 - 443	384 - 443
2	3	TRP	TRP	VAL	VAL	B	B	384 - 443	384 - 443
1	4	GLN	GLN	LYS	LYS	A	A	366 - 377	366 - 377
2	4	GLN	GLN	LYS	LYS	B	B	366 - 377	366 - 377

NCS ensembles :

ID
1
2
3
4

#1: Protein	ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN Mass: 51122.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q6GJJ0, UniProt: A0A7U7ETV2*PLUS
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-SM / SAMARIUM (III) ION Mass: 150.360 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Sm
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 43 % / Description: NONE
Crystal grow	pH: 8 Details: 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M ...Details: 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M TRIS-CL, PH8.0, 0.3 M MGCL2, 2.0% ETHYLENE GLYCOL, 19% PEG400 DILUTED WITH A 50MM PLP SOLUTION 1:10 (FINAL CONCENTRATIONS ABOUT 17% PEG400 AND 5MM PLP)

Crystal

Density Matthews: 2.1 Å³/Da / Density % sol: 43 % / Description: NONE

Crystal grow

pH: 8
Details: 20% PEG4000, 0.1 M TRIS-CL, PH8.0, 0.32 M MGCL2, 0.8% ETHYLENE GLYCOL. THE CRYSTAL WAS SOAKED WITH 20 MM SAMARIUM ACETATE AND 5MM PLP. THE CRYSTALS WERE CRYOPROTECTED WITH 22% PEG4000, 0.1M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 25, 2007 / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 2→29.17 Å / Num. obs: 50798 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / B_iso Wilson estimate: 0 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0090	refinement
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2→29.17 Å / Cor.coef. F_o:F_c: 0.906 / Cor.coef. F_o:F_c free: 0.868 / SU B: 14.06 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ONLY ORDERED FROM RESIDUE 5 TO 443. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27684	2713	5.1 %	RANDOM
R_work	0.22886	-	-	-
obs	0.23132	50798	99.16 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 9.754 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	-0.09 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 2→29.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6800	0	41	127	6968

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	7023
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4635
X-RAY DIFFRACTION	r_angle_refined_deg	1.125	1.966	9509
X-RAY DIFFRACTION	r_angle_other_deg	0.82	3	11430
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.65	5	839
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.348	25.392	319
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.938	15	1248
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.475	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1065
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	7608
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1300
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	0.349	1.5	4211
X-RAY DIFFRACTION	r_mcbond_other	0.089	1.5	1699
X-RAY DIFFRACTION	r_mcangle_it	0.626	2	6841
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.164	3	2812
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.609	4.5	2667
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1758	medium positional	0.34	0.5
1	2	B	1758	medium positional	0.34	0.5
2	1	A	2923	medium positional	0.39	0.5
2	2	B	2923	medium positional	0.39	0.5
3	1	A	812	medium positional	0.45	0.5
3	2	B	812	medium positional	0.45	0.5
4	1	A	167	medium positional	0.44	0.5
4	2	B	167	medium positional	0.44	0.5
1	1	A	1758	medium thermal	0.4	2
1	2	B	1758	medium thermal	0.4	2
2	1	A	2923	medium thermal	0.35	2
2	2	B	2923	medium thermal	0.35	2
3	1	A	812	medium thermal	0.32	2
3	2	B	812	medium thermal	0.32	2
4	1	A	167	medium thermal	0.27	2
4	2	B	167	medium thermal	0.27	2

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.359	185	-
R_work	0.314	3740	-
obs	-	-	98.69 %

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	0.9701	0.8439	0.5519	1.6199	0.1839	1.2452	0.1171	-0.1647	0.0882	0.2756	-0.0805	-0.0271	-0.1514	0.2085	-0.0366	0.1407	-0.0338	0.0138	0.1896	-0.0469	0.0852	9.177	-4.398	12.947
2	2.0258	1.5376	-0.5357	2.3312	-1.361	2.76	-0.0501	0.0879	-0.0341	-0.2755	0.0511	0.0808	0.2586	0.0988	-0.0009	0.0557	0.0138	-0.0175	0.056	-0.0274	0.0544	0.58	-18.469	-6.575
3	0.8779	0.264	-0.2251	1.2565	-0.3442	1.7831	0.0011	0.0651	-0.2292	-0.0421	-0.0621	-0.0018	0.1798	-0.0476	0.0609	0.0425	0.0036	-0.0165	0.0614	-0.017	0.0773	10.303	-18.804	3.498
4	0.1803	0.0078	0.2198	0.9259	-0.2689	1.3983	0.0376	-0.0647	-0.086	0.1168	-0.0489	-0.0329	0.1542	0.0702	0.0112	0.0933	0.0171	-0.0122	0.0958	0.0003	0.0952	6.328	-14.927	14.896
5	0.8464	0.0281	0.7796	0.5525	-0.0768	2.6369	0.0354	-0.0689	-0.0328	0.0967	0.0005	0.1015	0.0314	-0.2925	-0.0359	0.0824	-0.0065	0.0144	0.0841	-0.0061	0.1018	-12.96	-19.186	4.579
6	0.132	-0.0869	-0.3029	2.4145	-0.191	0.7753	0.0084	0.0479	-0.0137	0.2494	-0.0067	0.2731	-0.0187	-0.1531	-0.0017	0.1879	-0.0393	0.0503	0.2091	-0.0151	0.1514	0.843	6.018	18.04
7	1.4482	0.3978	-0.0403	2.0587	0.4899	1.0614	-0.051	0.2385	0.1044	-0.2482	0.0612	-0.0027	-0.0886	-0.042	-0.0101	0.0371	0.0054	-0.0075	0.0669	0.0157	0.091	4.658	15.489	-6.751
8	0.8769	0.4956	0.3841	1.2445	0.0943	1.2398	-0.0555	-0.0001	0.2859	-0.0603	-0.0246	0.0413	-0.1523	-0.0709	0.0801	0.0781	0.016	0.0262	0.0542	-0.0182	0.1483	-0.594	20.898	2.205
9	0.5598	0.3475	-0.1459	0.8369	0.0054	0.1689	0.0688	-0.0893	0.2359	0.1049	-0.0795	0.2077	-0.0984	-0.0257	0.0106	0.127	0.0159	-0.0048	0.093	-0.028	0.1647	4.628	19.274	12.179
10	0.8822	0.0981	-0.3559	0.9318	0.4255	2.5481	0.0537	0.1015	0.045	0.0112	0.0258	-0.1099	-0.0965	0.2782	-0.0796	0.0939	-0.0034	-0.0041	0.0997	0.0091	0.162	22.303	19.593	1.407
11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.6334	0.0858	-0.1576	0.4925	-0.1953	0.4818	-16.82	-27.882	-24.371
12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.5234	-0.0062	0.0076	0.3074	-0.1876	0.7369	-15.493	-29.103	-19.89
13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.2184	-0.012	-0.0251	0.1708	-0.0494	0.3693	-25.089	-30.058	-11.698
14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	1.3275	-0.071	0.1423	0.5842	0.0762	0.7452	6.576	15.439	-22.563
15	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	1.1317	-0.0677	-0.2095	0.5518	0.1925	1.0867	11.102	31.698	-16.716
16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0	0.5946	-0.0656	0.0207	0.5228	-0.0224	0.8485	28.306	40.116	13.595

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 95
2	X-RAY DIFFRACTION	2	A	96 - 156
3	X-RAY DIFFRACTION	3	A	157 - 230
4	X-RAY DIFFRACTION	4	A	231 - 290
5	X-RAY DIFFRACTION	5	A	291 - 443
6	X-RAY DIFFRACTION	6	B	5 - 69
7	X-RAY DIFFRACTION	7	B	70 - 153
8	X-RAY DIFFRACTION	8	B	154 - 226
9	X-RAY DIFFRACTION	9	B	227 - 303
10	X-RAY DIFFRACTION	10	B	304 - 443
11	X-RAY DIFFRACTION	11	A	1445
12	X-RAY DIFFRACTION	12	A	1446
13	X-RAY DIFFRACTION	13	A	1447
14	X-RAY DIFFRACTION	14	B	1445
15	X-RAY DIFFRACTION	15	B	1446
16	X-RAY DIFFRACTION	16	B	1447

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About Yorodumi

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Yorodumi