PDB-6fan: Crystal structure of putative CooT from Carboxydothermus hydrogen...

Basic information

• Entry: Database: PDB / ID: 6fan
• Title: Crystal structure of putative CooT from Carboxydothermus hydrogenoformans
• Components: CooT
• Keywords: METAL BINDING PROTEIN / Carbon monoxide dehydrogenase / nickel chaperone / maturation pathway
• Function / homology: CO dehydrogenase accessory protein CooT / CO dehydrogenase accessory protein CooT / RNA-binding protein
• Biological species: Carboxydothermus hydrogenoformans (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
• Authors: Cavazza, C. / Alfano, M.
• Citation: Journal: J.Biol.Inorg.Chem. / Year: 2018; Title: Biophysical and structural characterization of the putative nickel chaperone CooT from Carboxydothermus hydrogenoformans.; Authors: Alfano, M. / Perard, J. / Miras, R. / Catty, P. / Cavazza, C.

History

Deposition	Dec 15, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 28, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: CooT

B: CooT

C: CooT

D: CooT

E: CooT

F: CooT

hetero molecules

Summary:

• 44.7 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	44,662	14
Polymers	43,821	6
Non-polymers	841	8
Water	1,081	60

1

E: CooT

hetero molecules

A: CooT

Summary:

• defined by author
• Evidence: light scattering
• 14.9 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	14,909	5
Polymers	14,607	2
Non-polymers	302	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_346	-x-2,y-1/2,-z+1	1

2

A: CooT

E: CooT

hetero molecules

Summary:

• defined by author&software
• 14.9 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	14,909	5
Polymers	14,607	2
Non-polymers	302	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_356	-x-2,y+1/2,-z+1	1

Calculated values:

Buried area	1680 Å2
ΔGint	-14 kcal/mol
Surface area	7050 Å2
Method	PISA

3

B: CooT

F: CooT

hetero molecules

Summary:

• defined by author&software
• 14.9 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	14,909	5
Polymers	14,607	2
Non-polymers	302	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1720 Å2
ΔGint	-12 kcal/mol
Surface area	6940 Å2
Method	PISA

4

C: CooT

D: CooT

hetero molecules

Summary:

• defined by author&software
• 14.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	14,843	4
Polymers	14,607	2
Non-polymers	236	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	1720 Å2
ΔGint	-12 kcal/mol
Surface area	6960 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	41.261, 61.350, 81.118
Angle α, β, γ (deg.)	90.00, 100.41, 90.00
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	B
2	6	C
1	7	B
2	7	D
1	8	B
2	8	E
1	9	B
2	9	F
1	10	C
2	10	D
1	11	C
2	11	E
1	12	C
2	12	F
1	13	D
2	13	E
1	14	D
2	14	F
1	15	E
2	15	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	2 - 62
2	0	1	0	B	2 - 62
1	0	2	0	A	2 - 61
2	0	2	0	C	2 - 61
1	0	3	0	A	2 - 61
2	0	3	0	D	2 - 61
1	0	4	0	A	2 - 62
2	0	4	0	E	2 - 62
1	0	5	0	A	2 - 61
2	0	5	0	F	2 - 61
1	0	6	0	B	2 - 61
2	0	6	0	C	2 - 61
1	0	7	0	B	2 - 61
2	0	7	0	D	2 - 61
1	0	8	0	B	2 - 62
2	0	8	0	E	2 - 62
1	0	9	0	B	2 - 61
2	0	9	0	F	2 - 61
1	0	10	0	C	2 - 61
2	0	10	0	D	2 - 61
1	0	11	0	C	2 - 61
2	0	11	0	E	2 - 61
1	0	12	0	C	2 - 61
2	0	12	0	F	2 - 61
1	0	13	0	D	2 - 61
2	0	13	0	E	2 - 61
1	0	14	0	D	1 - 62
2	0	14	0	F	1 - 62
1	0	15	0	E	2 - 61
2	0	15	0	F	2 - 61

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

Components

#1: Protein

A B C D E F
CooT

Details:

Mass: 7303.479 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria)
Gene: CHY_0178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3AFN4

#2: Chemical

B-101 C-101 D-101 E-101
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL

Details:

Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM

#3: Chemical

B-102 B-103 E-102 E-103
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.3 ų/Da / Density % sol: 46.62 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop; Details: 47% (v/v) 2-methylpentane-2,4-diol, 2% (v/v) 2-methyl-2-propanol

Data collection

• Diffraction: Mean temperature: 93 K
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97979 Å
• Detector: Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2017
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97979 Å / Relative weight: 1
• Reflection: Resolution: 2→33.85 Å / Num. obs: 97738 / % possible obs: 97.6 % / Redundancy: 1.9 % / Net I/σ(I): 13.41
• Reflection shell: Resolution: 2→2.1 Å

Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→79.78 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.932 / SU B: 7.304 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.27517	1299	4.9 %	RANDOM
Rwork	0.23463	-	-	-
obs	0.23658	25451	98.74 %	-

• 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: 47.801 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.9 Å2	-0 Å2	-2.65 Å2
2-	-	2.4 Å2	0 Å2
3-	-	-	-0.49 Å2

Refinement step

Cycle: 1 / Resolution: 2→79.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2937	0	55	60	3052

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	3060
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.096	2.019	4096
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.821	5	374
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.871	23.986	143
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.839	15	625
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.65	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	490
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2169
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	5.08	4.678	1483
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	6.863	6.978	1846
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	5.756	5.01	1577
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	10.765	87.183	11005
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	3360	0.08
1	2	B	3360	0.08
2	1	A	3310	0.07
2	2	C	3310	0.07
3	1	A	3218	0.1
3	2	D	3218	0.1
4	1	A	3340	0.1
4	2	E	3340	0.1
5	1	A	3250	0.1
5	2	F	3250	0.1
6	1	B	3430	0.08
6	2	C	3430	0.08
7	1	B	3238	0.11
7	2	D	3238	0.11
8	1	B	3430	0.1
8	2	E	3430	0.1
9	1	B	3284	0.1
9	2	F	3284	0.1
10	1	C	3128	0.1
10	2	D	3128	0.1
11	1	C	3248	0.12
11	2	E	3248	0.12
12	1	C	3156	0.11
12	2	F	3156	0.11
13	1	D	3272	0.1
13	2	E	3272	0.1
14	1	D	3362	0.1
14	2	F	3362	0.1
15	1	E	3322	0.1
15	2	F	3322	0.1

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.396	97	-
Rwork	0.37	1886	-
obs	-	-	98.31 %