PDB-3cuc: CRYSTAL STRUCTURE OF A FIC DOMAIN CONTAINING SIGNALING PROTEIN (B...

ID or keywords:

Entry

Database: PDB / ID: 3cuc

Title

CRYSTAL STRUCTURE OF A FIC DOMAIN CONTAINING SIGNALING PROTEIN (BT_2513) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.71 A RESOLUTION

Components

Protein of unknown function with a Fic domain

Keywords

SIGNALING PROTEIN / FIC PROTEIN FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2

Function / homology

Function and homology information

Biological species

Bacteroides thetaiotaomicron VPI-5482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.71 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of Protein of Unknown Function with a Fic Domain (NP_811426.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.71 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Apr 16, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3	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 1.4	Feb 1, 2023	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Oct 30, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3cuc.cif.gz	115.6 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	3cuc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3cuc_validation.pdf.gz	432.1 KB	Display	wwPDB validaton report
Full document	3cuc_full_validation.pdf.gz	434.8 KB	Display
Data in XML	3cuc_validation.xml.gz	18.5 KB	Display
Data in CIF	3cuc_validation.cif.gz	24.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cu/3cuc ftp://data.pdbj.org/pub/pdb/validation_reports/cu/3cuc	HTTPS FTP

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Related structure data

Similar structure data	5gp1-3 6mod-d 3elw-d 3d0k-1 3f7d-d 6el6-d 4lyl-3 2p1d-d 6el9-d 5n8c-2 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
Other databases	TargetDB: 371850

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein of unknown function with a Fic domain

B: Protein of unknown function with a Fic domain

67.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein of unknown function with a Fic domain

defined by software
33.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein of unknown function with a Fic domain

defined by software
33.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	138.725, 138.725, 120.723
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	LYS	LYS	1	A	A	4 - 7	5 - 8
2	1	SER	SER	LYS	LYS	1	B	B	4 - 7	5 - 8
3	2	LEU	LEU	PHE	PHE	1	A	A	9 - 31	10 - 32
4	2	LEU	LEU	PHE	PHE	1	B	B	9 - 31	10 - 32
5	3	LEU	LEU	THR	THR	1	A	A	33 - 52	34 - 53
6	3	LEU	LEU	THR	THR	1	B	B	33 - 52	34 - 53
7	4	GLU	GLU	GLN	GLN	1	A	A	72 - 109	73 - 110
8	4	GLU	GLU	GLN	GLN	1	B	B	72 - 109	73 - 110
9	5	VAL	VAL	SER	SER	4	A	A	129 - 148	130 - 149
10	5	VAL	VAL	SER	SER	4	B	B	129 - 148	130 - 149
11	6	TYR	TYR	SER	SER	1	A	A	149 - 222	150 - 223
12	6	TYR	TYR	SER	SER	1	B	B	149 - 222	150 - 223
13	7	ASP	ASP	ILE	ILE	1	A	A	224 - 231	225 - 232
14	7	ASP	ASP	ILE	ILE	1	B	B	224 - 231	225 - 232
15	8	HIS	HIS	ASP	ASP	4	A	A	233 - 245	234 - 246
16	8	HIS	HIS	ASP	ASP	4	B	B	233 - 245	234 - 246
17	9	GLY	GLY	LEU	LEU	1	A	A	246 - 251	247 - 252
18	9	GLY	GLY	LEU	LEU	1	B	B	246 - 251	247 - 252
19	10	ASP	ASP	SER	SER	1	A	A	253 - 280	254 - 281
20	10	ASP	ASP	SER	SER	1	B	B	253 - 280	254 - 281

#1: Protein	Protein of unknown function with a Fic domain Mass: 33573.961 Da / Num. of mol.: 2 / Fragment: Residues 1-290 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Species: Bacteroides thetaiotaomicron / Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50 / Gene: NP_811426.1, BT_2513 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A4T4
Has protein modification	Y
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. THE CLONED CONSTRUCT CONTAINS RESIDUES 1-290 OF THE FULL LENGTH PROTEIN.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.99 Å³/Da / Density % sol: 75.37 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: NANODROP, 15.1% 2-methyl-2,4-pentanediol, 0.1M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 0.91837, 0.97954, 0.97882

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 5, 2008 / Details: Flat mirror (vertical focusing)

Radiation

Monochromator: Single crystal Si(111) bent (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	0.97954	1
3	0.97882	1

Reflection

Resolution: 2.71→29.273 Å / Num. obs: 36830 / % possible obs: 99.9 % / Redundancy: 5.6 % / B_iso Wilson estimate: 59.078 Å² / R_merge(I) obs: 0.155 / R_sym value: 0.155 / Net I/σ(I): 4.6

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
2.71-2.78	5.7	0.97	0.8	15415	2706	0.97	100
2.78-2.86	5.7	0.892	0.9	14746	2593	0.892	100
2.86-2.94	5.7	0.74	1	14613	2574	0.74	100
2.94-3.03	5.7	0.56	1.4	14149	2488	0.56	100
3.03-3.13	5.7	0.437	1.7	13616	2391	0.437	100
3.13-3.24	5.7	0.356	2.1	13373	2351	0.356	100
3.24-3.36	5.7	0.273	2.8	12732	2243	0.273	100
3.36-3.5	5.7	0.21	3.6	12288	2164	0.21	100
3.5-3.65	5.7	0.178	4.3	11931	2102	0.178	100
3.65-3.83	5.7	0.143	5.3	11285	1990	0.143	100
3.83-4.04	5.6	0.115	6.5	10684	1895	0.115	100
4.04-4.28	5.6	0.109	6.7	10181	1807	0.109	100
4.28-4.58	5.6	0.096	7.5	9582	1701	0.096	100
4.58-4.95	5.6	0.087	8	8872	1585	0.087	100
4.95-5.42	5.6	0.083	8.5	8192	1468	0.083	100
5.42-6.06	5.6	0.087	8.3	7449	1338	0.087	100
6.06-7	5.5	0.078	9.2	6525	1182	0.078	100
7-8.57	5.4	0.057	11.5	5504	1012	0.057	100
8.57-12.12	5.3	0.047	13	4267	806	0.047	100
12.12-29.273	4.8	0.052	8.8	2097	434	0.052	93.2

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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
MAR345	CCD	data collection
MOSFLM		data reduction
SHELXD		phasing
autoSHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.71→29.273 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.9 / SU B: 20.215 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.238
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. DENSITY FOR LOOP RESIDUES A133-154 IS POOR AND MODEL IS BUILT BASED ON NCS. 4. ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.248	1840	5 %	RANDOM
R_work	0.222	-	-	-
obs	0.224	36802	99.89 %	-

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: 43.724 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.09 Å²	0.54 Å²	0 Å²
2-	-	1.09 Å²	0 Å²
3-	-	-	-1.63 Å²

Refinement step

Cycle: LAST / Resolution: 2.71→29.273 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4221	0	0	0	4221

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4319
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2902
X-RAY DIFFRACTION	r_angle_refined_deg	1.021	1.966	5855
X-RAY DIFFRACTION	r_angle_other_deg	0.808	3	7095
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.85	5	527
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.006	24.703	202
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.48	15	748
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.212	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	649
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	4772
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	852
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	995
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	2767
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	2179
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	2178
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	67
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.174	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.276	0.2	24
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.076	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.067	3	2704
X-RAY DIFFRACTION	r_mcbond_other	0.201	3	1066
X-RAY DIFFRACTION	r_mcangle_it	1.869	5	4244
X-RAY DIFFRACTION	r_scbond_it	3.374	8	1843
X-RAY DIFFRACTION	r_scangle_it	5.041	11	1610

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
2762	TIGHT POSITIONAL	0.03	0.05
324	MEDIUM POSITIONAL	0.45	0.5
2762	TIGHT THERMAL	0.18	1
324	MEDIUM THERMAL	0.46	2

LS refinement shell

Resolution: 2.71→2.78 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	142	-
R_work	0.328	2563	-
all	-	2705	-
obs	-	-	99.96 %

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	3.2763	-0.6207	-0.7204	1.5192	0.0893	0.16	0.0975	0.7228	-0.054	-0.1124	0.1154	0.2063	0.0064	-0.4889	-0.2128	-0.0165	0.1037	0.0135	0.4913	0.1318	0.0247	22.3659	64.3689	21.0885
2	1.1664	-0.1195	-0.4176	0.7113	-0.2699	1.5133	-0.0037	-0.0993	-0.069	0.1303	0.0166	0.0989	-0.1135	-0.1603	-0.0128	-0.221	-0.0151	0.0015	-0.2096	-0.0012	-0.2022	62.1228	51.6956	25.4737

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	4 - 282	5 - 283
2	X-RAY DIFFRACTION	2	B	B	4 - 285	5 - 286

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