PDB-3hln: Crystal structure of ClpP A153C mutant with inter-heptamer disulf...

ID or keywords:

Entry

Database: PDB / ID: 3hln

Title

Crystal structure of ClpP A153C mutant with inter-heptamer disulfide bonds

Components

ATP-dependent Clp protease proteolytic subunit

Keywords

HYDROLASE / disulfide bond / disordered equatorial loops / ATP-binding / Nucleotide-binding / Protease / Serine protease / Stress response / Zymogen

Function / homology

Function and homology information

HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Kimber, M.S. / Yu, A.Y.H. / Borg, M. / Chan, H.S. / Houry, W.A.

Citation

Journal: Structure / Year: 2010
Title: Structural and Theoretical Studies Indicate that the Cylindrical Protease ClpP Samples Extended and Compact Conformations.
Authors: Kimber, M.S. / Yu, A.Y. / Borg, M. / Leung, E. / Chan, H.S. / Houry, W.A.

History

Deposition	May 27, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 28, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Oct 13, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3hln.cif.gz	846.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3hln.ent.gz	700.7 KB	Display	PDB format
PDBx/mmJSON format	3hln.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3hln_validation.pdf.gz	581.4 KB	Display	wwPDB validaton report
Full document	3hln_full_validation.pdf.gz	656.9 KB	Display
Data in XML	3hln_validation.xml.gz	91 KB	Display
Data in CIF	3hln_validation.cif.gz	134.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hl/3hln ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hln	HTTPS FTP

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Related structure data

Related structure data	2fzsS S: Starting model for refinement
Similar structure data	6nay-1 6nay-2 6naw-d 2zl0-d 6w9t-1 2f6i-1 2zl3-d 6vgk-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: ATP-dependent Clp protease proteolytic subunit

B: ATP-dependent Clp protease proteolytic subunit

C: ATP-dependent Clp protease proteolytic subunit

D: ATP-dependent Clp protease proteolytic subunit

E: ATP-dependent Clp protease proteolytic subunit

F: ATP-dependent Clp protease proteolytic subunit

G: ATP-dependent Clp protease proteolytic subunit

H: ATP-dependent Clp protease proteolytic subunit

I: ATP-dependent Clp protease proteolytic subunit

J: ATP-dependent Clp protease proteolytic subunit

K: ATP-dependent Clp protease proteolytic subunit

L: ATP-dependent Clp protease proteolytic subunit

M: ATP-dependent Clp protease proteolytic subunit

N: ATP-dependent Clp protease proteolytic subunit

O: ATP-dependent Clp protease proteolytic subunit

P: ATP-dependent Clp protease proteolytic subunit

Q: ATP-dependent Clp protease proteolytic subunit

R: ATP-dependent Clp protease proteolytic subunit

S: ATP-dependent Clp protease proteolytic subunit

T: ATP-dependent Clp protease proteolytic subunit

U: ATP-dependent Clp protease proteolytic subunit

V: ATP-dependent Clp protease proteolytic subunit

W: ATP-dependent Clp protease proteolytic subunit

X: ATP-dependent Clp protease proteolytic subunit

Y: ATP-dependent Clp protease proteolytic subunit

Z: ATP-dependent Clp protease proteolytic subunit

1: ATP-dependent Clp protease proteolytic subunit

2: ATP-dependent Clp protease proteolytic subunit

hetero molecules

606 kDa, 28 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP-dependent Clp protease proteolytic subunit

B: ATP-dependent Clp protease proteolytic subunit

C: ATP-dependent Clp protease proteolytic subunit

D: ATP-dependent Clp protease proteolytic subunit

E: ATP-dependent Clp protease proteolytic subunit

F: ATP-dependent Clp protease proteolytic subunit

G: ATP-dependent Clp protease proteolytic subunit

H: ATP-dependent Clp protease proteolytic subunit

I: ATP-dependent Clp protease proteolytic subunit

J: ATP-dependent Clp protease proteolytic subunit

K: ATP-dependent Clp protease proteolytic subunit

L: ATP-dependent Clp protease proteolytic subunit

M: ATP-dependent Clp protease proteolytic subunit

N: ATP-dependent Clp protease proteolytic subunit

hetero molecules

defined by author&software
303 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

O: ATP-dependent Clp protease proteolytic subunit

P: ATP-dependent Clp protease proteolytic subunit

Q: ATP-dependent Clp protease proteolytic subunit

R: ATP-dependent Clp protease proteolytic subunit

S: ATP-dependent Clp protease proteolytic subunit

T: ATP-dependent Clp protease proteolytic subunit

U: ATP-dependent Clp protease proteolytic subunit

V: ATP-dependent Clp protease proteolytic subunit

W: ATP-dependent Clp protease proteolytic subunit

X: ATP-dependent Clp protease proteolytic subunit

Y: ATP-dependent Clp protease proteolytic subunit

Z: ATP-dependent Clp protease proteolytic subunit

1: ATP-dependent Clp protease proteolytic subunit

2: ATP-dependent Clp protease proteolytic subunit

hetero molecules

defined by author&software
303 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	182.299, 182.299, 476.859
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	2	2 - 200
2	1	1	6	1	2 - 200
1	1	2	6	Z	2 - 200
2	1	2	6	1	2 - 200
1	1	3	6	A	2 - 200
2	1	3	6	1	2 - 200
1	1	4	6	B	2 - 200
2	1	4	6	1	2 - 200
1	1	5	6	C	2 - 200
2	1	5	6	1	2 - 200
1	1	6	6	D	2 - 200
2	1	6	6	1	2 - 200
1	1	7	6	E	2 - 200
2	1	7	6	1	2 - 200
1	1	8	6	F	2 - 200
2	1	8	6	1	2 - 200
1	1	9	6	G	2 - 200
2	1	9	6	1	2 - 200
1	1	10	6	H	2 - 200
2	1	10	6	1	2 - 200
1	1	11	6	I	2 - 200
2	1	11	6	1	2 - 200
1	1	12	6	J	2 - 200
2	1	12	6	1	2 - 200
1	1	13	6	K	2 - 200
2	1	13	6	1	2 - 200
1	1	14	6	L	2 - 200
2	1	14	6	1	2 - 200
1	1	15	6	M	2 - 200
2	1	15	6	1	2 - 200
1	1	16	6	N	2 - 200
2	1	16	6	1	2 - 200
1	1	17	6	O	2 - 200
2	1	17	6	1	2 - 200
1	1	18	6	P	2 - 200
2	1	18	6	1	2 - 200
1	1	19	6	Q	2 - 200
2	1	19	6	1	2 - 200
1	1	20	6	R	2 - 200
2	1	20	6	1	2 - 200
1	1	21	6	S	2 - 200
2	1	21	6	1	2 - 200
1	1	22	6	T	2 - 200
2	1	22	6	1	2 - 200
1	1	23	6	U	2 - 200
2	1	23	6	1	2 - 200
1	1	24	6	V	2 - 200
2	1	24	6	1	2 - 200
1	1	25	6	W	2 - 200
2	1	25	6	1	2 - 200
1	1	26	6	X	2 - 200
2	1	26	6	1	2 - 200
1	1	27	6	Y	2 - 200
2	1	27	6	1	2 - 200

NCS ensembles :

#1: Protein	... ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp / Caseinolytic protease / Protease Ti / Heat shock protein F21.5 Mass: 21618.928 Da / Num. of mol.: 28 / Fragment: UNP residues 15-207 / Mutation: A153C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0437, clpP, JW0427, lopP / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): SG1146(DE3)clpP / References: UniProt: P0A6G7, endopeptidase Clp
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca

#1: Protein

...
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp / Caseinolytic protease / Protease Ti / Heat shock protein F21.5

Mass: 21618.928 Da / Num. of mol.: 28 / Fragment: UNP residues 15-207 / Mutation: A153C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K-12 / Gene: b0437, clpP, JW0427, lopP / Plasmid: pET9a / Production host:

Escherichia coli (E. coli) / Strain (production host): SG1146(DE3)clpP / References: UniProt: P0A6G7, endopeptidase Clp

#2: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.78 Å³/Da / Density % sol: 67.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1 M 1,6-hexanediol, 0.1 M Sodium acetate pH 4.6, 10 mM CoCl2, 100 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2007
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 3.2→42.22 Å / Num. all: 148306 / Num. obs: 148306 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / R_sym value: 0.045 / Net I/σ(I): 14.2
Reflection shell	Resolution: 3.2→3.31 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.1 / R_sym value: 0.394 / % possible all: 91.7

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
REFMAC	5.2.0019	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2FZS

2fzs

Resolution: 3.2→42.22 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.922 / SU B: 49.832 / SU ML: 0.364 / Isotropic thermal model: ISOTROPIC + TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25274	7454	5 %	RANDOM
R_work	0.21342	-	-	-
obs	0.21542	140770	97.5 %	-
all	-	148224	-	-

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: 99.003 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.52 Å²	0.26 Å²	0 Å²
2-	-	0.52 Å²	0 Å²
3-	-	-	-0.78 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→42.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	35831	0	13	0	35844

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	36377
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	24985
X-RAY DIFFRACTION	r_angle_refined_deg	0.987	1.974	48959
X-RAY DIFFRACTION	r_angle_other_deg	0.794	3.001	60900
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.94	5	4498
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.109	23.92	1653
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.014	15	6800
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.749	15	280
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	5571
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	39974
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	7146
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	9332
X-RAY DIFFRACTION	r_nbd_other	0.171	0.2	26970
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	17592
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	20172
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	781
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.019	0.2	2
X-RAY DIFFRACTION	r_metal_ion_refined	0.031	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.165	0.2	68
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.174	0.2	143
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.191	0.2	10
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	0.247	1.5	23573
X-RAY DIFFRACTION	r_mcbond_other	0.031	1.5	9250
X-RAY DIFFRACTION	r_mcangle_it	0.44	2	36344
X-RAY DIFFRACTION	r_scbond_it	0.477	3	14541
X-RAY DIFFRACTION	r_scangle_it	0.798	4.5	12615
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	2	2163	loose positional	0.62	5
2	Z	2176	loose positional	0.75	5
3	A	2163	loose positional	0.62	5
4	B	2163	loose positional	0.76	5
5	C	2163	loose positional	0.66	5
6	D	2163	loose positional	0.64	5
7	E	2163	loose positional	0.63	5
8	F	2176	loose positional	0.51	5
9	G	2163	loose positional	0.63	5
10	H	2176	loose positional	0.53	5
11	I	2163	loose positional	0.71	5
12	J	2163	loose positional	0.78	5
13	K	2147	loose positional	0.58	5
14	L	2163	loose positional	0.7	5
15	M	2163	loose positional	0.66	5
16	N	2163	loose positional	0.73	5
17	O	2176	loose positional	0.67	5
18	P	2163	loose positional	0.65	5
19	Q	2163	loose positional	0.66	5
20	R	2163	loose positional	0.66	5
21	S	2163	loose positional	0.63	5
22	T	2147	loose positional	0.52	5
23	U	2163	loose positional	0.62	5
24	V	2176	loose positional	0.68	5
25	W	2147	loose positional	0.79	5
26	X	2148	loose positional	0.8	5
27	Y	2176	loose positional	0.79	5
1	2	2163	loose thermal	1.48	10
2	Z	2176	loose thermal	1.3	10
3	A	2163	loose thermal	2.32	10
4	B	2163	loose thermal	2.66	10
5	C	2163	loose thermal	3.59	10
6	D	2163	loose thermal	3.04	10
7	E	2163	loose thermal	1.52	10
8	F	2176	loose thermal	2.23	10
9	G	2163	loose thermal	0.82	10
10	H	2176	loose thermal	3.18	10
11	I	2163	loose thermal	1.13	10
12	J	2163	loose thermal	2.19	10
13	K	2147	loose thermal	0.84	10
14	L	2163	loose thermal	1.82	10
15	M	2163	loose thermal	2.53	10
16	N	2163	loose thermal	3.45	10
17	O	2176	loose thermal	2.54	10
18	P	2163	loose thermal	0.85	10
19	Q	2163	loose thermal	3.17	10
20	R	2163	loose thermal	4.36	10
21	S	2163	loose thermal	2.73	10
22	T	2147	loose thermal	2.96	10
23	U	2163	loose thermal	1.01	10
24	V	2176	loose thermal	1.33	10
25	W	2147	loose thermal	1.13	10
26	X	2148	loose thermal	1.48	10
27	Y	2176	loose thermal	4.17	10

LS refinement shell

Resolution: 3.2→3.281 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.369	519	-
R_work	0.3	9285	-
obs	-	-	88.99 %

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