PDB-2v19: Crystal structure of the T. thermophilus dodecin R45A mutant

ID or keywords:

Entry

Database: PDB / ID: 2v19

Title

Crystal structure of the T. thermophilus dodecin R45A mutant

Components

DODECIN

Keywords

FLAVOPROTEIN / FLAVIN BINDING PROTEIN / DODECINS / 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: 2.59 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 22, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2007	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2011	Group: Database references / Version format compliance
Revision 1.2	Jul 5, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3	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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2v19.cif.gz	189.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2v19.ent.gz	157.3 KB	Display	PDB format
PDBx/mmJSON format	2v19.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v1/2v19 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v19	HTTPS FTP

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Related structure data

Related structure data	2ux9C 2v18C 2v21C 1mogS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2ux9-1 2v18-d 2vyx-d 5ys2-2 2hwj-1 5fsb-3 2yj0-1 4dj3-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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: DODECIN

B: DODECIN

C: DODECIN

D: DODECIN

E: DODECIN

F: DODECIN

G: DODECIN

H: DODECIN

I: DODECIN

J: DODECIN

K: DODECIN

L: DODECIN

hetero molecules

104 kDa, 12 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)	67.294, 68.494, 229.891
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:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:
NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.9312, -0.32813, 0.15872), (-0.33314, 0.5895, -0.73587), (0.1479, -0.73812, -0.65826)	55.95205, -9.94296, -46.28741
2	given	(-0.07055, 0.97138, -0.22681), (-0.28941, -0.23752, -0.92727), (-0.9546, 0.00022, 0.29788)	12.85405, -10.1767, 3.74075
3	given	(-0.29806, 0.76462, -0.57141), (0.20752, 0.63621, 0.74308), (0.93172, 0.1029, -0.3483)	10.16242, 19.14417, -63.38848
4	given	(0.01912, 0.54248, 0.83985), (-0.82468, -0.46637, 0.32001), (0.56528, -0.69873, 0.43846)	44.85554, 41.27356, -25.11373
5	given	(-0.06747, -0.29786, -0.95222), (0.97437, -0.22496, 0.00133), (-0.21461, -0.92773, 0.3054)	1.42923, -14.98958, -7.53746
6	given	(-0.9546, -0.11753, -0.27374), (-0.11471, -0.703, 0.70188), (-0.27493, 0.70141, 0.6576)	42.26832, 36.65581, -8.44409
7	given	(0.88465, 0.45191, 0.11474), (0.45171, -0.89169, 0.02931), (0.11555, 0.0259, -0.99296)	2.76851, 4.31198, -61.10047
8	given	(0.02635, -0.82744, 0.56093), (0.54358, -0.45906, -0.7027), (0.83894, 0.32343, 0.43769)	47.16928, -22.64051, -39.7762
9	given	(0.35099, -0.90506, 0.24017), (-0.46748, 0.05287, 0.88242), (-0.81134, -0.422, -0.40453)	30.40783, 44.75162, -17.04535
10	given	(-0.30169, 0.21213, 0.92951), (0.76104, 0.64083, 0.10076), (-0.57428, 0.73779, -0.35478)	58.1334, -13.54142, -30.68601
11	given	(0.34709, -0.45498, -0.82007), (-0.90938, 0.05048, -0.41289), (0.22926, 0.88907, -0.39623)	-3.81682, 18.16955, -53.28222

#1: Protein	DODECIN / HYPOTHETICAL PROTEIN TTHA1431 Mass: 7542.619 Da / Num. of mol.: 12 / Fragment: RESIDUES 2-69 / Mutation: YES 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.: 10 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 45 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN C, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN E, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN F, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN G, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN H, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN I, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN J, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN K, ARG 45 TO ALA ENGINEERED RESIDUE IN CHAIN L, ARG 45 TO ALA
Nonpolymer details	COENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEOTIDE ...COENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES FLAVIN MONONUCLEOTIDE (FMN): FMN IS BOUND AS DIMERS ALONG THE TWOFOLD SYMMETRY AXES. DIMER B,H IS OMITTED SINCE ONLY RESIDUAL ELECTRON DENSITY IS OBSERVED
Sequence details	RESIDUE T69 NOT DEFINED IN ALL CHAINS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 57.2 % / Description: NONE
Crystal grow	Details: 0.1 M AMMONIUM SULFATE, 0.05 M SODIUM CACODYLATE, PH 6.5 AND 15% PEG 8000

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Data collection

Diffraction	Mean temperature: 11 K
Diffraction source	Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 22, 2005 / Details: OSMIC MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.58→25 Å / Num. obs: 32742 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.09 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.59→2.66 Å / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 3.5

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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: 2.59→25 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.915 / SU B: 18.527 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.908 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.234	1018	3.1 %	RANDOM
R_work	0.206	-	-	-
obs	0.207	31678	96.1 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.33 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.85 Å²	0 Å²	0 Å²
2-	-	-1.6 Å²	0 Å²
3-	-	-	-1.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.59→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6336	0	891	36	7263

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	7338
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4774
X-RAY DIFFRACTION	r_angle_refined_deg	1.002	2.117	10004
X-RAY DIFFRACTION	r_angle_other_deg	0.572	3	11662
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.928	5	798
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.487	24.167	288
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.381	15	1218
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.232	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1062
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	7428
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1290
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1135
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	4899
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	3343
X-RAY DIFFRACTION	r_nbtor_other	0.087	0.2	4000
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	172
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	0.255	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.396	0.2	57
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.177	0.2	8
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	1.528	1.5	5085
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.86	2	6282
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.049	3	4231
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.544	4.5	3722
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

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	868	tight positional	0.08	0.05
2	B	868	tight positional	0.09	0.05
3	C	868	tight positional	0.08	0.05
4	D	868	tight positional	0.08	0.05
5	E	868	tight positional	0.07	0.05
6	F	868	tight positional	0.08	0.05
7	G	868	tight positional	0.08	0.05
8	H	868	tight positional	0.08	0.05
9	I	868	tight positional	0.07	0.05
10	J	868	tight positional	0.07	0.05
11	K	868	tight positional	0.07	0.05
12	L	868	tight positional	0.07	0.05
1	A	92	medium positional	0.67	0.5
2	B	92	medium positional	0.82	0.5
3	C	92	medium positional	0.84	0.5
4	D	92	medium positional	1.06	0.5
5	E	92	medium positional	0.79	0.5
6	F	92	medium positional	2.04	0.5
7	G	92	medium positional	0.94	0.5
8	H	92	medium positional	1.03	0.5
9	I	92	medium positional	0.99	0.5
10	J	92	medium positional	1.14	0.5
11	K	92	medium positional	1.18	0.5
12	L	92	medium positional	1.25	0.5
1	A	868	tight thermal	0.3	0.5
2	B	868	tight thermal	0.31	0.5
3	C	868	tight thermal	0.27	0.5
4	D	868	tight thermal	0.25	0.5
5	E	868	tight thermal	0.26	0.5
6	F	868	tight thermal	0.29	0.5
7	G	868	tight thermal	0.27	0.5
8	H	868	tight thermal	0.26	0.5
9	I	868	tight thermal	0.25	0.5
10	J	868	tight thermal	0.26	0.5
11	K	868	tight thermal	0.26	0.5
12	L	868	tight thermal	0.24	0.5
1	A	92	medium thermal	2.15	4
2	B	92	medium thermal	2.47	4
3	C	92	medium thermal	2.73	4
4	D	92	medium thermal	2.65	4
5	E	92	medium thermal	1.99	4
6	F	92	medium thermal	1.97	4
7	G	92	medium thermal	3.44	4
8	H	92	medium thermal	2.63	4
9	I	92	medium thermal	2.31	4
10	J	92	medium thermal	1.62	4
11	K	92	medium thermal	2.81	4
12	L	92	medium thermal	2.15	4

LS refinement shell

Resolution: 2.59→2.66 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.336	51
R_work	0.361	1407

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