PDB-5y9n: Crystal structure of Pyrococcus furiosus PbaA (monoclinic form), ...

Basic information

• Entry: Database: PDB / ID: 5y9n
• Title: Crystal structure of Pyrococcus furiosus PbaA (monoclinic form), an archaeal homolog of proteasome-assembly chaperone
• Components: PbaA
• Keywords: CHAPERONE / PROTEASOME / PROTEASOME ACTIVATOR / PROTEASOME ASSEMBLY CHAPERONE
• Function / homology: Conserved hypothetical protein CHP00061 / PAC-like subunit / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Proteasome assembly chaperone family protein
• Biological species: Pyrococcus furiosus (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
• Authors: Yagi-Utsumi, M. / Sikdar, A. / Kozai, T. / Inoue, R. / Sugiyama, M. / Uchihashi, T. / Satoh, T. / Kato, K.

Funding support

Japan, 4items

Organization	Grant number	Country
Ministry of Education, Culture, Sports, Science and Technology (Japan)	17K15441	Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)	25102001	Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)	25102008	Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)	15H02491	Japan

• Citation: Journal: Protein Eng. Des. Sel. / Year: 2018; Title: Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation; Authors: Yagi-Utsumi, M. / Sikdar, A. / Kozai, T. / Inoue, R. / Sugiyama, M. / Uchihashi, T. / Yagi, H. / Satoh, T. / Kato, K.

History

Deposition	Aug 26, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Assembly

Deposited unit

A: PbaA

B: PbaA

C: PbaA

D: PbaA

E: PbaA

F: PbaA

G: PbaA

H: PbaA

I: PbaA

J: PbaA

hetero molecules

Summary:

• 274 kDa, 10 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	274,203	20
Polymers	273,848	10
Non-polymers	355	10
Water	2,540	141

1

A: PbaA

B: PbaA

C: PbaA

D: PbaA

E: PbaA

hetero molecules

Summary:

• defined by author&software
• Evidence: gel filtration, mass spectrometry
• 137 kDa, 5 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	137,208	13
Polymers	136,924	5
Non-polymers	284	8
Water	90	5

Symmetry operations:

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

Calculated values:

Buried area	9460 Å2
ΔGint	-84 kcal/mol
Surface area	58180 Å2
Method	PISA

2

F: PbaA

G: PbaA

H: PbaA

I: PbaA

J: PbaA

hetero molecules

Summary:

• defined by author&software
• 137 kDa, 5 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	136,995	7
Polymers	136,924	5
Non-polymers	71	2
Water	90	5

Symmetry operations:

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

Calculated values:

Buried area	9460 Å2
ΔGint	-85 kcal/mol
Surface area	57920 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	92.690, 200.940, 92.760
Angle α, β, γ (deg.)	90.00, 110.96, 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	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	B
2	10	C
1	11	B
2	11	D
1	12	B
2	12	E
1	13	B
2	13	F
1	14	B
2	14	G
1	15	B
2	15	H
1	16	B
2	16	I
1	17	B
2	17	J
1	18	C
2	18	D
1	19	C
2	19	E
1	20	C
2	20	F
1	21	C
2	21	G
1	22	C
2	22	H
1	23	C
2	23	I
1	24	C
2	24	J
1	25	D
2	25	E
1	26	D
2	26	F
1	27	D
2	27	G
1	28	D
2	28	H
1	29	D
2	29	I
1	30	D
2	30	J
1	31	E
2	31	F
1	32	E
2	32	G
1	33	E
2	33	H
1	34	E
2	34	I
1	35	E
2	35	J
1	36	F
2	36	G
1	37	F
2	37	H
1	38	F
2	38	I
1	39	F
2	39	J
1	40	G
2	40	H
1	41	G
2	41	I
1	42	G
2	42	J
1	43	H
2	43	I
1	44	H
2	44	J
1	45	I
2	45	J

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 5 - 242 / Label seq-ID: 8 - 245

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	B	B
2	10	C	C
1	11	B	B
2	11	D	D
1	12	B	B
2	12	E	E
1	13	B	B
2	13	F	F
1	14	B	B
2	14	G	G
1	15	B	B
2	15	H	H
1	16	B	B
2	16	I	I
1	17	B	B
2	17	J	J
1	18	C	C
2	18	D	D
1	19	C	C
2	19	E	E
1	20	C	C
2	20	F	F
1	21	C	C
2	21	G	G
1	22	C	C
2	22	H	H
1	23	C	C
2	23	I	I
1	24	C	C
2	24	J	J
1	25	D	D
2	25	E	E
1	26	D	D
2	26	F	F
1	27	D	D
2	27	G	G
1	28	D	D
2	28	H	H
1	29	D	D
2	29	I	I
1	30	D	D
2	30	J	J
1	31	E	E
2	31	F	F
1	32	E	E
2	32	G	G
1	33	E	E
2	33	H	H
1	34	E	E
2	34	I	I
1	35	E	E
2	35	J	J
1	36	F	F
2	36	G	G
1	37	F	F
2	37	H	H
1	38	F	F
2	38	I	I
1	39	F	F
2	39	J	J
1	40	G	G
2	40	H	H
1	41	G	G
2	41	I	I
1	42	G	G
2	42	J	J
1	43	H	H
2	43	I	I
1	44	H	H
2	44	J	J
1	45	I	I
2	45	J	J

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

Components

#1: Protein

A B C D E F G H I J
PbaA

Details:

Mass: 27384.826 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0015 / Plasmid: PET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U4Q9

#2: Chemical

A-301 B-301 C-301 C-302 D-301 D-302 E-301 E-302 G-301 H-301
ChemComp-CL / CHLORIDE ION / Chloride

Details:

Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl

#3: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.95 ų/Da / Density % sol: 58.24 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 ; Details: 30% MPD, 0.1 M sodium acetate (pH 4.6), and 20 mM calcium chloride

Data collection

• Diffraction: Mean temperature: 95 K
• Diffraction source: Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
• Detector: Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2011
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1 Å / Relative weight: 1
• Reflection: Resolution: 2.55→50 Å / Num. obs: 101818 / % possible obs: 99 % / Redundancy: 3.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.043 / Net I/σ(I): 17.5
• Reflection shell: Resolution: 2.55→2.71 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.675 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 16291 / CC_1/2: 0.812 / % possible all: 98.3

Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WZ2

3wz2

Resolution: 2.55→20 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.947 / SU B: 13.35 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.508 / ESU R Free: 0.276 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.24039	5085	5 %	RANDOM
Rwork	0.20777	-	-	-
obs	0.20939	96609	99 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 83.267 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	1.03 Å2	0 Å2	1.05 Å2
2-	-	-3.45 Å2	0 Å2
3-	-	-	1.25 Å2

Refinement step

Cycle: 1 / Resolution: 2.55→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18670	0	10	141	18821

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	19020
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	18630
X-RAY DIFFRACTION	r_angle_refined_deg	1.549	2.001	25690
X-RAY DIFFRACTION	r_angle_other_deg	0.952	3	43270
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.951	5	2370
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.377	24.875	800
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.595	15	3540
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.85	15	100
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2890
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	20810
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3570
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	6.836	7.852	9510
X-RAY DIFFRACTION	r_mcbond_other	6.836	7.852	9509
X-RAY DIFFRACTION	r_mcangle_it	9.292	11.787	11870
X-RAY DIFFRACTION	r_mcangle_other	9.292	11.787	11871
X-RAY DIFFRACTION	r_scbond_it	7.76	8.81	9510
X-RAY DIFFRACTION	r_scbond_other	7.759	8.81	9510
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	11.504	12.814	13820
X-RAY DIFFRACTION	r_long_range_B_refined	13.633	91.62	20263
X-RAY DIFFRACTION	r_long_range_B_other	13.633	91.62	20264
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	14668	0.03
1	2	B	14668	0.03
2	1	A	14710	0.03
2	2	C	14710	0.03
3	1	A	14686	0.03
3	2	D	14686	0.03
4	1	A	14742	0.03
4	2	E	14742	0.03
5	1	A	14722	0.04
5	2	F	14722	0.04
6	1	A	14752	0.02
6	2	G	14752	0.02
7	1	A	14682	0.04
7	2	H	14682	0.04
8	1	A	14728	0.03
8	2	I	14728	0.03
9	1	A	14700	0.03
9	2	J	14700	0.03
10	1	B	14662	0.04
10	2	C	14662	0.04
11	1	B	14656	0.04
11	2	D	14656	0.04
12	1	B	14666	0.04
12	2	E	14666	0.04
13	1	B	14660	0.04
13	2	F	14660	0.04
14	1	B	14698	0.03
14	2	G	14698	0.03
15	1	B	14634	0.05
15	2	H	14634	0.05
16	1	B	14660	0.04
16	2	I	14660	0.04
17	1	B	14662	0.04
17	2	J	14662	0.04
18	1	C	14652	0.03
18	2	D	14652	0.03
19	1	C	14716	0.03
19	2	E	14716	0.03
20	1	C	14674	0.04
20	2	F	14674	0.04
21	1	C	14712	0.03
21	2	G	14712	0.03
22	1	C	14686	0.04
22	2	H	14686	0.04
23	1	C	14690	0.04
23	2	I	14690	0.04
24	1	C	14686	0.03
24	2	J	14686	0.03
25	1	D	14712	0.04
25	2	E	14712	0.04
26	1	D	14694	0.04
26	2	F	14694	0.04
27	1	D	14710	0.03
27	2	G	14710	0.03
28	1	D	14668	0.04
28	2	H	14668	0.04
29	1	D	14690	0.04
29	2	I	14690	0.04
30	1	D	14702	0.03
30	2	J	14702	0.03
31	1	E	14704	0.04
31	2	F	14704	0.04
32	1	E	14758	0.03
32	2	G	14758	0.03
33	1	E	14694	0.04
33	2	H	14694	0.04
34	1	E	14736	0.04
34	2	I	14736	0.04
35	1	E	14712	0.03
35	2	J	14712	0.03
36	1	F	14722	0.04
36	2	G	14722	0.04
37	1	F	14678	0.05
37	2	H	14678	0.05
38	1	F	14694	0.04
38	2	I	14694	0.04
39	1	F	14694	0.04
39	2	J	14694	0.04
40	1	G	14730	0.04
40	2	H	14730	0.04
41	1	G	14736	0.03
41	2	I	14736	0.03
42	1	G	14714	0.02
42	2	J	14714	0.02
43	1	H	14686	0.04
43	2	I	14686	0.04
44	1	H	14672	0.04
44	2	J	14672	0.04
45	1	I	14708	0.03
45	2	J	14708	0.03

LS refinement shell

Resolution: 2.551→2.617 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.386	360	-
Rwork	0.381	6848	-
obs	-	-	96.48 %