PDB-2v18: Crystal structure of the T. thermophilus dodecin

ID or keywords:

Entry

Database: PDB / ID: 2v18

Title

Crystal structure of the T. thermophilus dodecin

Components

DODECIN

Keywords

FLAVOPROTEIN /

HYPOTHETICAL PROTEIN / FLAVIN BINDING PROTEIN / DODECINS /

COENZYME A / FLAVIN DIMER / FLAVOPROTEIN 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	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 3, 2011	Group: Database references / Derived calculations / Other
Revision 1.3	Jul 5, 2017	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4	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

-
Download

PDBx/mmCIF format	2v18.cif.gz	185.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2v18.ent.gz	154.7 KB	Display	PDB format
PDBx/mmJSON format	2v18.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v1/2v18 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v18	HTTPS FTP

-
Related structure data

Related structure data	2ux9C 2v19C 2v21C 1mogS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2ux9-1 2vyx-d 2yj0-1 2deg-1 6r1e-1 2v19-d 2cz8-2 3qn0-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

-
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)	67.481, 98.038, 137.595
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	(0.06101, -0.90002, -0.43155), (-0.47519, 0.35403, -0.80552), (0.87777, 0.25421, -0.40608)	75.01335, 68.2186, 23.22009
2	given	(0.06235, -0.46562, 0.88279), (-0.9037, 0.34906, 0.24794), (-0.42359, -0.81324, -0.39902)	6.93078, 38.0041, 96.07857
3	given	(-0.69871, -0.52281, -0.48834), (-0.50984, -0.11496, 0.85255), (-0.50186, 0.84466, -0.18623)	119.61303, -14.67936, 88.31556
4	given	(0.63379, -0.2922, -0.71619), (0.54591, -0.48699, 0.68178), (-0.54799, -0.82308, -0.14913)	57.33044, -64.22738, 90.07703
5	given	(-0.2358, 0.77242, -0.58971), (0.33445, 0.63426, 0.69704), (0.91244, -0.03287, -0.40789)	98.27059, -54.10136, 21.73809
6	given	(0.6, 0.17273, 0.78113), (0.17566, -0.98103, 0.08201), (0.78048, 0.088, -0.61896)	-18.22406, -12.53655, 39.80697
7	given	(-0.46017, 0.8566, 0.2334), (-0.8504, -0.5008, 0.16134), (0.25508, -0.12424, 0.9589)	68.40688, 40.01682, -12.0124
8	given	(0.63724, 0.54591, -0.54398), (-0.29641, -0.47794, -0.82687), (-0.71138, 0.68816, -0.14275)	47.56391, 60.21171, 97.84086
9	given	(-0.8954, 0.33701, -0.29099), (0.33963, 0.09435, -0.93581), (-0.28793, -0.93676, -0.19894)	119.74323, 29.79404, 78.20866
10	given	(-0.22382, 0.32479, 0.91892), (0.76546, 0.6422, -0.04054), (-0.6033, 0.69433, -0.39235)	20.36069, -39.88252, 104.64338
11	given	(-0.46174, -0.84693, 0.26363), (0.85538, -0.50382, -0.12037), (0.23476, 0.16993, 0.95708)	68.38116, -40.09285, -11.04261

#1: Protein	DODECIN / HYPOTHETICAL PROTEIN TTHA1431 Mass: 7628.735 Da / Num. of mol.: 12 / Fragment: RESIDUES 2-69 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 / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	COENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES. COA TRIMER A,H,L IS ...COENZYME A (COA): COA IS BOUND AS TRIMERS ALONG THE THREEFOLD SYMMETRY AXES. COA TRIMER A,H,L IS OMITTED SINCE ONLY RESIDUAL DENSITY WAS OBSERVED FLAVIN MONONUCLEOTIDE (FMN): FMN IS BOUND AS DIMERS ALONG THE TWOFOLD SYMMETRY AXES.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 50.2 % / Description: NONE
Crystal grow	Details: 0.2 M SODIUM CITRATE, 0.1 M TRIS/HCL, PH 7.5, 25% PEG 400

-
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 28, 2003 / 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: 2.6→24.8 Å / Num. obs: 22085 / % possible obs: 76 % / Observed criterion σ(I): 0 / Redundancy: 2.75 % / R_merge(I) obs: 0.08 / Net I/σ(I): 19
Reflection shell	Resolution: 2.59→2.73 Å / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 3.9

-
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→24.76 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.907 / SU B: 29.146 / SU ML: 0.316 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.244	1125	5.1 %	RANDOM
R_work	0.219	-	-	-
obs	0.22	20911	76.2 %	-

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: 52.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.22 Å²	0 Å²	0 Å²
2-	-	0.12 Å²	0 Å²
3-	-	-	-0.33 Å²

Refinement step

Cycle: LAST / Resolution: 2.59→24.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6372	0	804	25	7201

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	7290
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	4845
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	2.108	9915
X-RAY DIFFRACTION	r_angle_other_deg	0.801	3	11781
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.662	5	792
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.361	23.6	300
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.585	15	1248
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.258	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	1044
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	7449
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1332
X-RAY DIFFRACTION	r_nbd_refined	0.179	0.2	1065
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	4802
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	3264
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	3902
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.183	0.2	118
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	0.257	0.2	36
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.301	0.2	70
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.527	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	0.522	1.5	5137
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.579	2	6252
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.993	3	4297
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.738	4.5	3663
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	880	tight positional	0.02	0.05
2	B	880	tight positional	0.03	0.05
3	C	880	tight positional	0.02	0.05
4	D	880	tight positional	0.03	0.05
5	E	880	tight positional	0.03	0.05
6	F	880	tight positional	0.02	0.05
7	G	880	tight positional	0.03	0.05
8	H	880	tight positional	0.02	0.05
9	I	880	tight positional	0.03	0.05
10	J	880	tight positional	0.03	0.05
11	K	880	tight positional	0.03	0.05
12	L	880	tight positional	0.02	0.05
1	A	70	medium positional	0.69	0.5
2	B	70	medium positional	1.1	0.5
3	C	70	medium positional	1.39	0.5
4	D	70	medium positional	0.75	0.5
5	E	70	medium positional	0.84	0.5
6	F	70	medium positional	1.34	0.5
7	G	70	medium positional	1.36	0.5
8	H	70	medium positional	0.79	0.5
9	I	70	medium positional	0.94	0.5
10	J	70	medium positional	0.83	0.5
11	K	70	medium positional	1.54	0.5
12	L	70	medium positional	0.91	0.5
1	A	880	tight thermal	0.13	1
2	B	880	tight thermal	0.14	1
3	C	880	tight thermal	0.14	1
4	D	880	tight thermal	0.13	1
5	E	880	tight thermal	0.14	1
6	F	880	tight thermal	0.14	1
7	G	880	tight thermal	0.14	1
8	H	880	tight thermal	0.11	1
9	I	880	tight thermal	0.13	1
10	J	880	tight thermal	0.13	1
11	K	880	tight thermal	0.13	1
12	L	880	tight thermal	0.12	1
1	A	70	medium thermal	0.16	2
2	B	70	medium thermal	0.34	2
3	C	70	medium thermal	0.26	2
4	D	70	medium thermal	0.32	2
5	E	70	medium thermal	0.26	2
6	F	70	medium thermal	0.33	2
7	G	70	medium thermal	0.39	2
8	H	70	medium thermal	0.27	2
9	I	70	medium thermal	0.18	2
10	J	70	medium thermal	0.3	2
11	K	70	medium thermal	0.26	2
12	L	70	medium thermal	0.21	2

LS refinement shell

Resolution: 2.59→2.73 Å / Total num. of bins used: 10 /

	R_factor	Num. reflection
R_free	0.388	75
R_work	0.373	1129

Refinement TLS params.

Method: refined / Origin x: 55.491 Å / Origin y: 0.733 Å / Origin z: 51.37 Å

	11	12	13	21	22	23	31	32	33
T	-0.5226 Å²	0.0053 Å²	0.0009 Å²	-	-0.4011 Å²	0.0177 Å²	-	-	-0.0786 Å²
L	1.1943 °²	-0.188 °²	-0.1424 °²	-	1.6793 °²	0.3252 °²	-	-	0.8155 °²
S	-0.0207 Å °	0.1642 Å °	0.0978 Å °	-0.1055 Å °	0.0192 Å °	-0.0563 Å °	-0.0109 Å °	0.0474 Å °	0.0015 Å °

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	1	B	2 - 68
3	X-RAY DIFFRACTION	1	C	2 - 68
4	X-RAY DIFFRACTION	1	D	2 - 68
5	X-RAY DIFFRACTION	1	E	2 - 68
6	X-RAY DIFFRACTION	1	F	2 - 68
7	X-RAY DIFFRACTION	1	G	2 - 68
8	X-RAY DIFFRACTION	1	H	2 - 68
9	X-RAY DIFFRACTION	1	I	2 - 68
10	X-RAY DIFFRACTION	1	J	2 - 68
11	X-RAY DIFFRACTION	1	K	2 - 68
12	X-RAY DIFFRACTION	1	L	2 - 68

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi