PDB-8p3m: The structure of thiocyanate dehydrogenase mutant form with Lys 2...

Basic information

• Entry: Database: PDB / ID: 8p3m
• Title: The structure of thiocyanate dehydrogenase mutant form with Lys 281 replaced by Ala from Thioalkalivibrio paradoxus
• Components: Twin-arginine translocation signal domain-containing protein
• Keywords: OXIDOREDUCTASE / Thiocyanate dehydrogenase / Thioalkalivibrio paradoxus / Recombinant protein / Surface amino acid residue mutation
• Function / homology: Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / BORIC ACID / COPPER (II) ION / Twin-arginine translocation signal domain-containing protein
• Biological species: Thioalkalivibrio paradoxus ARh 1 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
• Authors: Varfolomeeva, L.A. / Polyakov, K.M. / Komolov, A.S. / Rakitina, T.V. / Dergousova, N.I. / Dorovatovskii, P.V. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.

Funding support

Russian Federation, 1items

Organization	Grant number	Country
Russian Science Foundation	23-74-30004	Russian Federation

• Citation: Journal: Crystallography Reports / Year: 2023; Title: Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals; Authors: Varfolomeeva, L.A. / Polyakov, K.M. / Komolov, A.S. / Rakitina, T.V. / Dergousova, N.I. / Dorovatovskii, P.V. / Boyko, K.M. / Tikhonova, T.V. / Popov, V.O.

History

Deposition	May 18, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

Assembly

Deposited unit

A: Twin-arginine translocation signal domain-containing protein

D: Twin-arginine translocation signal domain-containing protein

G: Twin-arginine translocation signal domain-containing protein

J: Twin-arginine translocation signal domain-containing protein

M: Twin-arginine translocation signal domain-containing protein

P: Twin-arginine translocation signal domain-containing protein

S: Twin-arginine translocation signal domain-containing protein

V: Twin-arginine translocation signal domain-containing protein

Y: Twin-arginine translocation signal domain-containing protein

2: Twin-arginine translocation signal domain-containing protein

5: Twin-arginine translocation signal domain-containing protein

8: Twin-arginine translocation signal domain-containing protein

x: Twin-arginine translocation signal domain-containing protein

e: Twin-arginine translocation signal domain-containing protein

h: Twin-arginine translocation signal domain-containing protein

k: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

• 883 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	882,950	69
Polymers	879,114	16
Non-polymers	3,836	53
Water	43,596	2420

1

A: Twin-arginine translocation signal domain-containing protein

D: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

• defined by author&software
• Evidence: gel filtration
• 111 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,555	11
Polymers	109,889	2
Non-polymers	666	9
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	6410 Å2
ΔGint	-116 kcal/mol
Surface area	28520 Å2
Method	PISA

2

G: Twin-arginine translocation signal domain-containing protein

J: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,335	8
Polymers	109,889	2
Non-polymers	446	6
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	6050 Å2
ΔGint	-109 kcal/mol
Surface area	28340 Å2
Method	PISA

3

M: Twin-arginine translocation signal domain-containing protein

P: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,455	10
Polymers	109,889	2
Non-polymers	565	8
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	6200 Å2
ΔGint	-118 kcal/mol
Surface area	28280 Å2
Method	PISA

4

S: Twin-arginine translocation signal domain-containing protein

V: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,358	9
Polymers	109,889	2
Non-polymers	469	7
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	6070 Å2
ΔGint	-108 kcal/mol
Surface area	28050 Å2
Method	PISA

5

Y: Twin-arginine translocation signal domain-containing protein

2: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,335	8
Polymers	109,889	2
Non-polymers	446	6
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	6010 Å2
ΔGint	-107 kcal/mol
Surface area	28260 Å2
Method	PISA

6

5: Twin-arginine translocation signal domain-containing protein

8: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,335	8
Polymers	109,889	2
Non-polymers	446	6
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	6070 Å2
ΔGint	-107 kcal/mol
Surface area	28200 Å2
Method	PISA

7

x: Twin-arginine translocation signal domain-containing protein

e: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,239	7
Polymers	109,889	2
Non-polymers	350	5
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	5870 Å2
ΔGint	-95 kcal/mol
Surface area	28210 Å2
Method	PISA

8

h: Twin-arginine translocation signal domain-containing protein

k: Twin-arginine translocation signal domain-containing protein

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	110,335	8
Polymers	109,889	2
Non-polymers	446	6
Water	36	2

Symmetry operations:

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

Calculated values:

Buried area	6030 Å2
ΔGint	-105 kcal/mol
Surface area	28190 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	98.150, 142.420, 294.400
Angle α, β, γ (deg.)	90.00, 90.07, 90.00
Int Tables number	4
Space group name H-M	P1211

Components

Protein , 1 types, 16 molecules A D G J M P S V Y 2 5 8 x e h k

#1: Protein

A D G J M P S V Y 2 5 8 x e h k
Twin-arginine translocation signal domain-containing protein / Thiocyanate dehydrogenase

Details:

Mass: 54944.594 Da / Num. of mol.: 16 / Mutation: K281A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria)
Gene: THITH_13335 / Production host: Escherichia coli (E. coli) / References: UniProt: W0DP94

Non-polymers , 5 types, 2473 molecules

#2: Chemical

A-701 A-705 D-601 G-701 J-601 M-701 P-701 P-702 S-601 V-601 Y-601 2-701 5-601 8-701 x-601 h-601 k-701
ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄

#3: Chemical

A-702 D-602 ChemComp-BO3 / BORIC ACID

Details:

Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH₃O₃

#4: Chemical

A-703 A-704 D-603 D-604 G-702 G-703 J-602 J-603 M-702 M-703 P-703 P-704 S-602 S-603 V-602 V-603 Y-602 Y-603 2-702 2-703 ...
ChemComp-CU / COPPER (II) ION

Details:

Mass: 63.546 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION

#5: Chemical

P-705 V-604 ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 2420 / Source method: isolated from a natural source / Formula: H₂O

Details

• Has ligand of interest: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.34 ų/Da / Density % sol: 47.45 %
• Crystal grow: Temperature: 288 K / Method: vapor diffusion, hanging drop; Details: 0.5 M (NH4)2SO4, 0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.7 M Li2SO4

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
• Detector: Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2019
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1 Å / Relative weight: 1
• Reflection: Resolution: 2.07→49.12 Å / Num. obs: 485243 / % possible obs: 98.8 % / Redundancy: 2.92 % / CC_1/2: 0.991 / R_merge(I) obs: 0.125 / R_rim(I) all: 0.153 / Net I/σ(I): 6.91

Reflection shell

Resolution (Å)	Rmerge(I) obs	Num. unique obs	CC1/2	Rrim(I) all	Diffraction-ID
2.07-2.1	0.813	20586	0.408	0.993	1
2.1-2.15	0.712	31825	0.467	0.872	1
2.15-2.25	0.591	55489	0.564	0.729	1
2.25-2.5	0.408	102772	0.782	0.497	1
2.5-3	0.219	116138	0.93	0.27	1
3-4	0.08	90948	0.989	0.099	1
4-5	0.051	32776	0.994	0.063	1
5-6	0.05	14547	0.994	0.062	1
6-10	0.045	15800	0.996	0.055	1
10-49.12	0.035	4362	0.997	0.043	1

Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XSCALE		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→49.12 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.931 / SU B: 6.136 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.23365	24463	5 %	RANDOM
Rwork	0.17884	-	-	-
obs	0.1816	460779	98.79 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 30.317 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.73 Å2	0 Å2	-0.26 Å2
2-	-	-0.09 Å2	0 Å2
3-	-	-	0.82 Å2

Refinement step

Cycle: 1 / Resolution: 2.07→49.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	57885	0	127	2420	60432

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.012	59715
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.816	1.635	81505
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.725	5	7456
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.8	23.108	2902
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.296	15	9030
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.914	15	268
X-RAY DIFFRACTION	r_chiral_restr	0.184	0.2	7633
X-RAY DIFFRACTION	r_gen_planes_refined	0.018	0.02	46332
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	4.531	2.934	29872
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.388	4.371	37312
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.021	3.109	29843
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	8.106	39.964	91419
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

LS refinement shell

Resolution: 2.07→2.124 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.345	1793	-
Rwork	0.295	34342	-
obs	-	-	99.72 %