PDB-3dfe: Crystal structure of a Putative Pii-Like Signaling Protein (YP_32...

ID or keywords:

Entry

Database: PDB / ID: 3dfe

Title

Crystal structure of a Putative Pii-Like Signaling Protein (YP_323533.1) from ANABAENA VARIABILIS ATCC 29413 at 2.35 A resolution

Components

Putative Pii-Like Signaling Protein

Keywords

SIGNALING PROTEIN / YP_323533.1 / A Putative Pii-Like Signaling Protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2

Function / homology

Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / Uncharacterized protein

Function and homology information

Biological species

Anabaena variabilis ATCC 29413 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.35 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of a Putative Pii-Like Signaling Protein (YP_323533.1) from ANABAENA VARIABILIS ATCC 29413 at 2.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jun 11, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 11, 2017	Group: Data collection / Refinement description / Category: reflns_shell / software Item: _reflns_shell.percent_possible_all / _software.classification / _software.name
Revision 1.3	Oct 25, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Feb 1, 2023	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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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PDBx/mmCIF format	3dfe.cif.gz	99.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3dfe_validation.pdf.gz	504.4 KB	Display	wwPDB validaton report
Full document	3dfe_full_validation.pdf.gz	518.2 KB	Display
Data in XML	3dfe_validation.xml.gz	17.9 KB	Display
Data in CIF	3dfe_validation.cif.gz	25.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/df/3dfe ftp://data.pdbj.org/pub/pdb/validation_reports/df/3dfe	HTTPS FTP

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Related structure data

Similar structure data	6n4a-2 1o67-1 4c3m-d 4q9c-1 2ahn-d 5ls3-1 1o67-3 4mxn-4 6tqa-3 4e22-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 - HomologyF&H Search
Other databases	TargetDB: 378258

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Putative Pii-Like Signaling Protein

B: Putative Pii-Like Signaling Protein

C: Putative Pii-Like Signaling Protein

D: Putative Pii-Like Signaling Protein

E: Putative Pii-Like Signaling Protein

F: Putative Pii-Like Signaling Protein

hetero molecules

73 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Putative Pii-Like Signaling Protein

E: Putative Pii-Like Signaling Protein

F: Putative Pii-Like Signaling Protein

defined by author&software
Evidence: gel filtration, light scattering
36.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Putative Pii-Like Signaling Protein

B: Putative Pii-Like Signaling Protein

C: Putative Pii-Like Signaling Protein

hetero molecules

defined by author&software
Evidence: gel filtration, light scattering
36.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.491, 78.749, 65.544
Angle α, β, γ (deg.)	90.000, 100.560, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	GLY	2	A	A	3 - 31	4 - 32
2	1	LYS	GLY	2	B	B	3 - 31	4 - 32
3	1	LYS	GLY	2	C	C	3 - 31	4 - 32
4	1	LYS	GLY	2	D	D	3 - 31	4 - 32
5	1	LYS	GLY	2	E	E	3 - 31	4 - 32
6	1	LYS	GLY	2	F	F	3 - 31	4 - 32
7	2	TYR	TYR	5	A	A	32	33
8	2	TYR	TYR	5	B	B	32	33
9	2	TYR	TYR	5	C	C	32	33
10	2	TYR	TYR	5	D	D	32	33
11	2	TYR	TYR	5	E	E	32	33
12	2	TYR	TYR	5	F	F	32	33
13	3	THR	ASP	2	A	A	33 - 77	34 - 78
14	3	THR	ASP	2	B	B	33 - 77	34 - 78
15	3	THR	ASP	2	C	C	33 - 77	34 - 78
16	3	THR	ASP	2	D	D	33 - 77	34 - 78
17	3	THR	ASP	2	E	E	33 - 77	34 - 78
18	3	THR	ASP	2	F	F	33 - 77	34 - 78
19	4	GLN	GLN	5	A	A	78	79
20	4	GLN	GLN	5	B	B	78	79
21	4	GLN	GLN	5	C	C	78	79
22	4	GLN	GLN	5	D	D	78	79
23	4	GLN	GLN	5	E	E	78	79
24	4	GLN	GLN	5	F	F	78	79
25	5	VAL	PHE	2	A	A	79 - 83	80 - 84
26	5	VAL	PHE	2	B	B	79 - 83	80 - 84
27	5	VAL	PHE	2	C	C	79 - 83	80 - 84
28	5	VAL	PHE	2	D	D	79 - 83	80 - 84
29	5	VAL	PHE	2	E	E	79 - 83	80 - 84
30	5	VAL	PHE	2	F	F	79 - 83	80 - 84
31	6	PHE	TYR	5	A	A	84 - 92	85 - 93
32	6	PHE	TYR	5	B	B	84 - 92	85 - 93
33	6	PHE	TYR	5	C	C	84 - 92	85 - 93
34	6	PHE	TYR	5	D	D	84 - 92	85 - 93
35	6	PHE	TYR	5	E	E	84 - 92	85 - 93
36	6	PHE	TYR	5	F	F	84 - 92	85 - 93
37	7	ILE	LEU	2	A	A	93 - 99	94 - 100
38	7	ILE	LEU	2	B	B	93 - 99	94 - 100
39	7	ILE	LEU	2	C	C	93 - 99	94 - 100
40	7	ILE	LEU	2	D	D	93 - 99	94 - 100
41	7	ILE	LEU	2	E	E	93 - 99	94 - 100
42	7	ILE	LEU	2	F	F	93 - 99	94 - 100
43	8	TYR	GLY	5	A	A	100 - 101	101 - 102
44	8	TYR	GLY	5	B	B	100 - 101	101 - 102
45	8	TYR	GLY	5	C	C	100 - 101	101 - 102
46	8	TYR	GLY	5	D	D	100 - 101	101 - 102
47	8	TYR	GLY	5	E	E	100 - 101	101 - 102
48	8	TYR	GLY	5	F	F	100 - 101	101 - 102

Details

AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS WHICH FORM TWO TRIMERS BASED ON CRYSTAL PACKING ANALYSIS. SIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

#1: Protein	Putative Pii-Like Signaling Protein Mass: 12152.575 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria) Gene: YP_323533.1, Ava_3028 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M8P8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 35.0000% 2-propanol, 5.0000% PEG-1000, 35.0000% 2-propanol, 5.0000% PEG-1000, 0.1M Citrate pH 5.5, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.91837,0.97854

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 2008 / Details: Flat mirror (vertical focusing)

Radiation

Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.91837	1
2	0.97854	1

Reflection

Resolution: 2.35→29.814 Å / Num. obs: 26560 / % possible obs: 99.9 % / Redundancy: 3.8 % / B_iso Wilson estimate: 57.051 Å² / R_merge(I) obs: 0.059 / R_sym value: 0.059 / Net I/σ(I): 7.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.35-2.41	3.8	0.606	1.3	7380	1948	0.606	100
2.41-2.48	3.8	0.55	1.4	7219	1911	0.55	100
2.48-2.55	3.8	0.49	1.6	7065	1870	0.49	100
2.55-2.63	3.8	0.389	2	6791	1793	0.389	100
2.63-2.71	3.8	0.282	2.7	6563	1730	0.282	100
2.71-2.81	3.8	0.238	3.2	6419	1693	0.238	100
2.81-2.91	3.8	0.174	4.3	6192	1633	0.174	100
2.91-3.03	3.8	0.13	5.7	5923	1563	0.13	100
3.03-3.17	3.8	0.103	7	5824	1533	0.103	100
3.17-3.32	3.8	0.08	8.3	5430	1434	0.08	100
3.32-3.5	3.8	0.067	8.8	5158	1361	0.067	100
3.5-3.72	3.8	0.055	10.8	4946	1304	0.055	100
3.72-3.97	3.8	0.05	11.7	4658	1232	0.05	100
3.97-4.29	3.8	0.042	13.7	4278	1130	0.042	100
4.29-4.7	3.8	0.038	15.5	3987	1053	0.038	100
4.7-5.25	3.8	0.039	13.8	3622	962	0.039	100
5.25-6.07	3.7	0.041	14.1	3145	840	0.041	100
6.07-7.43	3.7	0.043	13.7	2655	718	0.043	100
7.43-10.51	3.6	0.034	16.2	2010	557	0.034	98.7
10.51-29.82	3.4	0.038	15.2	1000	295	0.038	92.4

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHENIX		refinement
SHELX		phasing
MolProbity	3beta29	model building
SCALA		data scaling
PDB_EXTRACT	3.004	data extraction
MOSFLM		data reduction
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.35→29.814 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.926 / SU B: 21.096 / SU ML: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.242
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.267	1339	5 %	RANDOM
R_work	0.224	-	-	-
obs	0.227	26543	99.93 %	-

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: 48.862 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.43 Å²	0 Å²	4.08 Å²
2-	-	-1.25 Å²	0 Å²
3-	-	-	-1.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→29.814 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3582	0	8	21	3611

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3618
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	2201
X-RAY DIFFRACTION	r_angle_refined_deg	1.621	1.96	4908
X-RAY DIFFRACTION	r_angle_other_deg	0.997	3	5437
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.294	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.407	25.573	131
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.554	15	574
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.273	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	628
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4028
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	696
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	640
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	2125
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1824
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	1990
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	60
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.277	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.161	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	0.734	2	2515
X-RAY DIFFRACTION	r_mcbond_other	0.323	2	1010
X-RAY DIFFRACTION	r_mcangle_it	1.089	3	3828
X-RAY DIFFRACTION	r_scbond_it	0.981	2	1310
X-RAY DIFFRACTION	r_scangle_it	1.248	3	1080

Refine LS restraints NCS

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	397	TIGHT POSITIONAL	0.07	0.05
2	B	397	TIGHT POSITIONAL	0.04	0.05
3	C	397	TIGHT POSITIONAL	0.03	0.05
4	D	397	TIGHT POSITIONAL	0.05	0.05
5	E	397	TIGHT POSITIONAL	0.03	0.05
6	F	397	TIGHT POSITIONAL	0.04	0.05
1	A	392	MEDIUM POSITIONAL	0.29	0.5
2	B	392	MEDIUM POSITIONAL	0.25	0.5
3	C	392	MEDIUM POSITIONAL	0.21	0.5
4	D	392	MEDIUM POSITIONAL	0.3	0.5
5	E	392	MEDIUM POSITIONAL	0.2	0.5
6	F	392	MEDIUM POSITIONAL	0.26	0.5
1	A	105	LOOSE POSITIONAL	0.39	5
2	B	105	LOOSE POSITIONAL	0.33	5
3	C	105	LOOSE POSITIONAL	0.34	5
4	D	105	LOOSE POSITIONAL	0.43	5
5	E	105	LOOSE POSITIONAL	0.37	5
6	F	105	LOOSE POSITIONAL	0.37	5
1	A	397	TIGHT THERMAL	0.23	0.5
2	B	397	TIGHT THERMAL	0.11	0.5
3	C	397	TIGHT THERMAL	0.08	0.5
4	D	397	TIGHT THERMAL	0.11	0.5
5	E	397	TIGHT THERMAL	0.08	0.5
6	F	397	TIGHT THERMAL	0.08	0.5
1	A	392	MEDIUM THERMAL	1.08	2
2	B	392	MEDIUM THERMAL	0.61	2
3	C	392	MEDIUM THERMAL	0.53	2
4	D	392	MEDIUM THERMAL	0.55	2
5	E	392	MEDIUM THERMAL	0.48	2
6	F	392	MEDIUM THERMAL	0.36	2
1	A	105	LOOSE THERMAL	1.76	10
2	B	105	LOOSE THERMAL	0.73	10
3	C	105	LOOSE THERMAL	1.03	10
4	D	105	LOOSE THERMAL	1.43	10
5	E	105	LOOSE THERMAL	1.21	10
6	F	105	LOOSE THERMAL	0.86	10

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	110	-
R_work	0.283	1823	-
all	-	1933	-
obs	-	-	100 %

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	5.1469	1.0126	-2.6883	9.0858	1.9417	9.2673	-0.5047	-0.2404	-0.3062	-0.4902	-0.0974	0.1662	0.2909	-0.8675	0.6021	-0.4944	-0.0158	-0.1767	-0.1291	0.0286	-0.2766	-63.9924	9.6425	-4.2856
2	2.5269	-0.2571	-0.1652	3.6373	-0.9569	12.6472	-0.1528	0.5119	-0.5022	-0.5263	0.0301	0.0424	0.2506	0.194	0.1227	-0.0946	-0.0633	0.0973	-0.1749	-0.0995	-0.1545	-53.7225	8.6435	-22.2901
3	8.2533	-4.6	-4.4541	7.751	3.8962	5.4146	0.2325	0.3164	0.5603	-0.8975	-0.0364	0.0651	-1.1654	-0.2121	-0.1961	0.183	0.0642	0.0283	-0.2098	0.0397	-0.185	-60.2425	27.2471	-14.886
4	3.0687	0.7205	-1.0654	4.3696	3.3454	13.3096	0.0556	-0.3124	-0.2302	0.5848	-0.1934	0.0199	0.5798	0.4323	0.1377	-0.1088	0.0009	0.0835	-0.227	0.0453	-0.219	-45.4626	11.2404	20.9128
5	6.9509	3.9672	-3.0423	6.0712	-2.5331	5.6615	0.4572	-0.3774	0.6168	0.6441	-0.266	0.0031	-1.0645	0.4765	-0.1912	0.1661	-0.157	0.1372	-0.166	-0.0319	-0.0303	-37.4977	29.209	13.7662
6	2.555	-0.359	0.011	10.3449	-0.52	6.489	0.0362	0.0877	-0.0632	-0.2923	0.0966	-0.6101	0.1686	1.1242	-0.1327	-0.1573	0.0803	0.1302	0.0316	-0.0091	-0.0328	-32.4834	10.7884	4.9884

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 101	3 - 102
2	X-RAY DIFFRACTION	2	B	B	1 - 101	2 - 102
3	X-RAY DIFFRACTION	3	C	C	3 - 101	4 - 102
4	X-RAY DIFFRACTION	4	D	D	1 - 101	2 - 102
5	X-RAY DIFFRACTION	5	E	E	2 - 101	3 - 102
6	X-RAY DIFFRACTION	6	F	F	3 - 101	4 - 102

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Yorodumi