PDB-2v21: Crystal structure of the T. thermophilus dodecin in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 2v21

Title

Crystal structure of the T. thermophilus dodecin in complex with prebound FMN

Components

HYPOTHETICAL PROTEIN TTHA1431

Keywords

FLAVOPROTEIN / HYPOTHETICAL PROTEIN / FLAVIN BINDING PROTEIN / DODECINS / COENZYME A / FLAVIN DIMER / PUTATIVE STORAGE PROTEIN

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

THERMUS THERMOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Meissner, B. / Essen, L.-O.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: The Dodecin from Thermus Thermophilus, a Bifunctional Cofactor Storage Protein.
Authors: Meissner, B. / Schleicher, E. / Weber, S. / Essen, L.-O.

History

Deposition	May 31, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 3, 2011	Group: Database references / Derived calculations / Other
Revision 1.3	Feb 22, 2012	Group: Other
Revision 1.4	Jul 5, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2v21.cif.gz	92 KB	Display	PDBx/mmCIF format
PDB format	pdb2v21.ent.gz	72.5 KB	Display	PDB format
PDBx/mmJSON format	2v21.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2v21_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	2v21_full_validation.pdf.gz	1.3 MB	Display
Data in XML	2v21_validation.xml.gz	15.8 KB	Display
Data in CIF	2v21_validation.cif.gz	21.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v2/2v21 ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v21	HTTPS FTP

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Related structure data

Related structure data	2ux9C 2v18C 2v19C 1mogS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2dev-1 2deg-1 2deh-1 3oqt-3 6ri3-1 3onr-d 2cz8-2 2yiz-1 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

Deposited unit

A: HYPOTHETICAL PROTEIN TTHA1431

B: HYPOTHETICAL PROTEIN TTHA1431

C: HYPOTHETICAL PROTEIN TTHA1431

D: HYPOTHETICAL PROTEIN TTHA1431

E: HYPOTHETICAL PROTEIN TTHA1431

F: HYPOTHETICAL PROTEIN TTHA1431

hetero molecules

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

1

A: HYPOTHETICAL PROTEIN TTHA1431

B: HYPOTHETICAL PROTEIN TTHA1431

C: HYPOTHETICAL PROTEIN TTHA1431

D: HYPOTHETICAL PROTEIN TTHA1431

E: HYPOTHETICAL PROTEIN TTHA1431

F: HYPOTHETICAL PROTEIN TTHA1431

hetero molecules

A: HYPOTHETICAL PROTEIN TTHA1431

B: HYPOTHETICAL PROTEIN TTHA1431

C: HYPOTHETICAL PROTEIN TTHA1431

D: HYPOTHETICAL PROTEIN TTHA1431

E: HYPOTHETICAL PROTEIN TTHA1431

F: HYPOTHETICAL PROTEIN TTHA1431

hetero molecules

defined by author&software
95.9 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.765, 65.765, 202.408
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:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
1	2	A
2	2	C
3	2	F

NCS domain segments:

Dom-ID	Component-ID	Ens-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	1	GLY	GLY	GLU	GLU	1	A	A	2 - 15	2 - 15
2	1	1	GLY	GLY	GLU	GLU	1	B	B	2 - 15	2 - 15
3	1	1	GLY	GLY	GLU	GLU	1	C	C	2 - 15	2 - 15
4	1	1	GLY	GLY	GLU	GLU	1	D	D	2 - 15	2 - 15
5	1	1	GLY	GLY	GLU	GLU	1	E	E	2 - 15	2 - 15
6	1	1	GLY	GLY	GLU	GLU	1	F	F	2 - 15	2 - 15
1	2	1	GLU	GLU	GLU	GLU	2	A	A	16	16
2	2	1	GLU	GLU	GLU	GLU	2	B	B	16	16
3	2	1	GLU	GLU	GLU	GLU	2	C	C	16	16
4	2	1	GLU	GLU	GLU	GLU	2	D	D	16	16
5	2	1	GLU	GLU	GLU	GLU	2	E	E	16	16
6	2	1	GLU	GLU	GLU	GLU	2	F	F	16	16
1	3	1	GLY	GLY	ALA	ALA	1	A	A	17 - 29	17 - 29
2	3	1	GLY	GLY	ALA	ALA	1	B	B	17 - 29	17 - 29
3	3	1	GLY	GLY	ALA	ALA	1	C	C	17 - 29	17 - 29
4	3	1	GLY	GLY	ALA	ALA	1	D	D	17 - 29	17 - 29
5	3	1	GLY	GLY	ALA	ALA	1	E	E	17 - 29	17 - 29
6	3	1	GLY	GLY	ALA	ALA	1	F	F	17 - 29	17 - 29
1	4	1	ARG	ARG	ARG	ARG	2	A	A	30	30
2	4	1	ARG	ARG	ARG	ARG	2	B	B	30	30
3	4	1	ARG	ARG	ARG	ARG	2	C	C	30	30
4	4	1	ARG	ARG	ARG	ARG	2	D	D	30	30
5	4	1	ARG	ARG	ARG	ARG	2	E	E	30	30
6	4	1	ARG	ARG	ARG	ARG	2	F	F	30	30
1	5	1	LYS	LYS	LEU	LEU	1	A	A	31 - 33	31 - 33
2	5	1	LYS	LYS	LEU	LEU	1	B	B	31 - 33	31 - 33
3	5	1	LYS	LYS	LEU	LEU	1	C	C	31 - 33	31 - 33
4	5	1	LYS	LYS	LEU	LEU	1	D	D	31 - 33	31 - 33
5	5	1	LYS	LYS	LEU	LEU	1	E	E	31 - 33	31 - 33
6	5	1	LYS	LYS	LEU	LEU	1	F	F	31 - 33	31 - 33
1	6	1	ARG	ARG	ARG	ARG	2	A	A	34	34
2	6	1	ARG	ARG	ARG	ARG	2	B	B	34	34
3	6	1	ARG	ARG	ARG	ARG	2	C	C	34	34
4	6	1	ARG	ARG	ARG	ARG	2	D	D	34	34
5	6	1	ARG	ARG	ARG	ARG	2	E	E	34	34
6	6	1	ARG	ARG	ARG	ARG	2	F	F	34	34
1	7	1	HIS	HIS	GLY	GLY	1	A	A	35 - 49	35 - 49
2	7	1	HIS	HIS	GLY	GLY	1	B	B	35 - 49	35 - 49
3	7	1	HIS	HIS	GLY	GLY	1	C	C	35 - 49	35 - 49
4	7	1	HIS	HIS	GLY	GLY	1	D	D	35 - 49	35 - 49
5	7	1	HIS	HIS	GLY	GLY	1	E	E	35 - 49	35 - 49
6	7	1	HIS	HIS	GLY	GLY	1	F	F	35 - 49	35 - 49
1	8	1	GLU	GLU	GLU	GLU	2	A	A	50	50
2	8	1	GLU	GLU	GLU	GLU	2	B	B	50	50
3	8	1	GLU	GLU	GLU	GLU	2	C	C	50	50
4	8	1	GLU	GLU	GLU	GLU	2	D	D	50	50
5	8	1	GLU	GLU	GLU	GLU	2	E	E	50	50
6	8	1	GLU	GLU	GLU	GLU	2	F	F	50	50
1	9	1	ALA	ALA	GLU	GLU	1	A	A	51 - 67	51 - 67
2	9	1	ALA	ALA	GLU	GLU	1	B	B	51 - 67	51 - 67
3	9	1	ALA	ALA	GLU	GLU	1	C	C	51 - 67	51 - 67
4	9	1	ALA	ALA	GLU	GLU	1	D	D	51 - 67	51 - 67
5	9	1	ALA	ALA	GLU	GLU	1	E	E	51 - 67	51 - 67
6	9	1	ALA	ALA	GLU	GLU	1	F	F	51 - 67	51 - 67
1	10	1	GLU	GLU	GLU	GLU	4	A	A	68	68
2	10	1	GLU	GLU	GLU	GLU	4	B	B	68	68
3	10	1	GLU	GLU	GLU	GLU	4	C	C	68	68
4	10	1	GLU	GLU	GLU	GLU	4	D	D	68	68
5	10	1	GLU	GLU	GLU	GLU	4	E	E	68	68
6	10	1	GLU	GLU	GLU	GLU	4	F	F	68	68
1	1	2	FMN	FMN	FMN	FMN	4	A	G	101
2	1	2	FMN	FMN	FMN	FMN	4	C	I	101
3	1	2	FMN	FMN	FMN	FMN	4	F	J	101

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.1232, 0.45534, -0.88175), (-0.93635, -0.34767, -0.04871), (-0.32874, 0.81963, 0.46919)	107.05479, 66.72353, 40.41164
2	given	(-0.12318, -0.9316, -0.34197), (0.45853, -0.35903, 0.81292), (-0.8801, -0.05667, 0.4714)	89.66434, -58.05132, 78.68407
3	given	(-0.67197, 0.33065, 0.66267), (0.33566, -0.66163, 0.67051), (0.66014, 0.673, 0.33361)	62.05007, -41.54006, -9.6479
4	given	(-0.35535, -0.93227, -0.0678), (0.47251, -0.11657, -0.87358), (0.80651, -0.34247, 0.48193)	89.47807, 24.34116, -18.33639
5	given	(-0.45634, 0.35215, -0.81715), (0.11487, 0.93398, 0.33834), (0.88236, 0.06053, -0.46667)	123.8833, -23.20238, 22.08135

#1: Protein	HYPOTHETICAL PROTEIN TTHA1431 / DODECIN Mass: 7759.931 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q5SIE3
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUE T69 NOT DEFINED

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.2 % / Description: NONE
Crystal grow	Details: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, 30% MPD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 23, 2002 / Details: OSMIC MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.4→19.9 Å / Num. obs: 18248 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / R_merge(I) obs: 0.07 / Net I/σ(I): 23.3
Reflection shell	Resolution: 2.4→2.46 Å / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 3.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOG

1mog

Resolution: 2.4→19.87 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.919 / SU B: 18.586 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.262	1076	5.9 %	RANDOM
R_work	0.225	-	-	-
obs	0.227	17102	99.9 %	-

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: 62.42 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.03 Å²	0 Å²	0 Å²
2-	-	-0.03 Å²	0 Å²
3-	-	-	0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3181	0	95	13	3289

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	3316
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2294
X-RAY DIFFRACTION	r_angle_refined_deg	0.955	2.011	4463
X-RAY DIFFRACTION	r_angle_other_deg	0.752	3	5566
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.316	5	396
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.428	23.557	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.194	15	622
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.833	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	494
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3599
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	666
X-RAY DIFFRACTION	r_nbd_refined	0.176	0.2	439
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	2299
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	1501
X-RAY DIFFRACTION	r_nbtor_other	0.079	0.2	1886
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.095	0.2	62
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	0.162	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.197	0.2	45
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.159	0.2	16
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	0.376	1.5	1967
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.747	2	3123
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.078	3	1487
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.862	4.5	1340
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	839	tight positional	0.02	0.05
1	2	B	839	tight positional	0.02	0.05
1	3	C	839	tight positional	0.02	0.05
1	4	D	839	tight positional	0.02	0.05
1	5	E	839	tight positional	0.02	0.05
1	6	F	839	tight positional	0.02	0.05
1	1	A	61	medium positional	0.86	0.5
1	2	B	61	medium positional	0.56	0.5
1	3	C	61	medium positional	1.03	0.5
1	4	D	61	medium positional	0.54	0.5
1	5	E	61	medium positional	0.44	0.5
1	6	F	61	medium positional	0.51	0.5
2	1	A	41	medium positional	0.12	0.5
2	2	C	41	medium positional	0.1	0.5
2	3	F	41	medium positional	0.12	0.5
1	1	A	839	tight thermal	0.05	0.5
1	2	B	839	tight thermal	0.04	0.5
1	3	C	839	tight thermal	0.05	0.5
1	4	D	839	tight thermal	0.04	0.5
1	5	E	839	tight thermal	0.04	0.5
1	6	F	839	tight thermal	0.04	0.5
1	1	A	61	medium thermal	0.18	2
1	2	B	61	medium thermal	0.15	2
1	3	C	61	medium thermal	0.34	2
1	4	D	61	medium thermal	0.18	2
1	5	E	61	medium thermal	0.17	2
1	6	F	61	medium thermal	0.12	2
2	1	A	41	medium thermal	0.24	2
2	2	C	41	medium thermal	0.17	2
2	3	F	41	medium thermal	0.26	2

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.278	75
R_work	0.277	1218

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	3.8439	1.5787	0.1234	10.8801	2.0366	3.368	0.1471	-0.2021	-0.0856	0.1347	0.0466	0.7332	0.0742	-0.5858	-0.1938	-0.2814	-0.0503	0.0801	-0.1331	0.114	-0.1837	38.129	8.0854	59.3108
2	7.4765	0.0066	1.7693	2.937	-0.7479	3.8237	0.1688	-0.7099	-0.2635	0.7785	-0.0338	-0.1024	0.2065	0.304	-0.135	0.102	-0.0331	-0.0751	-0.0997	-0.0093	-0.2968	57.1887	4.4875	72.5143
3	2.6518	0.116	1.5723	6.3941	-3.393	8.5464	0.1269	-0.202	0.5271	0.6265	-0.0374	0.0027	-0.8423	0.1432	-0.0896	-0.1296	-0.0461	0.147	-0.2864	-0.0863	-0.1528	53.733	25.3767	62.281
4	4.5908	-1.4992	2.7277	4.2819	-3.201	10.4781	0.1842	0.6204	-0.2829	-0.5125	-0.251	-0.6974	0.5353	0.8965	0.0668	-0.2227	0.0156	0.0652	0.0422	-0.1033	-0.046	78.1799	5.8183	40.1992
5	6.3156	-3.063	-4.8721	5.7866	2.9919	8.011	0.4252	-0.32	0.6709	0.1212	0.0731	-0.7445	-0.7817	0.7467	-0.4983	-0.2289	-0.2066	-0.0463	-0.1142	-0.0806	-0.0281	73.2124	23.1821	55.1147
6	3.4874	0.7437	-0.0643	9.9857	-1.1086	3.7199	0.0633	-0.5927	-0.2604	0.805	0.0198	-0.7274	0.3883	0.6828	-0.0831	-0.16	0.0528	-0.186	0.1176	0.0334	-0.1055	75.5887	1.2761	63.3039

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 68
2	X-RAY DIFFRACTION	2	B	2 - 68
3	X-RAY DIFFRACTION	3	C	2 - 68
4	X-RAY DIFFRACTION	4	D	2 - 68
5	X-RAY DIFFRACTION	5	E	2 - 68
6	X-RAY DIFFRACTION	6	F	2 - 68

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