PDB-8xqu: The Crystal Structure of ClpC1-NTD from Biortus.

ID or keywords:

Entry

Database: PDB / ID: 8xqu

Title

The Crystal Structure of ClpC1-NTD from Biortus.

Components

ATP-dependent Clp protease ATP-binding subunit ClpC1

Keywords

CHAPERONE / ATP-dependent specificity component of the Clp protease. Degrades anti-sigma-E factor RseA

Function / homology

FORMIC ACID / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.

Funding support

1items

Citation

Journal: To Be Published
Title: The Crystal Structure of ClpC1-NTD from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Ni, C.

History

Deposition	Jan 5, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 6, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8xqu.cif.gz	92.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8xqu.ent.gz	55 KB	Display	PDB format
PDBx/mmJSON format	8xqu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xqu_validation.pdf.gz	445.4 KB	Display	wwPDB validaton report
Full document	8xqu_full_validation.pdf.gz	445.6 KB	Display
Data in XML	8xqu_validation.xml.gz	8.8 KB	Display
Data in CIF	8xqu_validation.cif.gz	11.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xq/8xqu ftp://data.pdbj.org/pub/pdb/validation_reports/xq/8xqu	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: ATP-dependent Clp protease ATP-binding subunit ClpC1

hetero molecules

16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	56.286, 56.286, 111.669
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-367- HOH
2	1	A-383- HOH

#1: Protein	ATP-dependent Clp protease ATP-binding subunit ClpC1 Mass: 16002.403 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: prokaryote coculture (bacteria)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.19 Å³/Da / Density % sol: 61.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4.0M Na formate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.1806 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 13, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1806 Å / Relative weight: 1
Reflection	Resolution: 1.85→43.72 Å / Num. obs: 18178 / % possible obs: 100 % / Redundancy: 9.5 % / R_merge(I) obs: 0.036 / Net I/σ(I): 29.9
Reflection shell	Resolution: 1.85→1.89 Å / R_merge(I) obs: 0.843 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1113

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→43.72 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.964 / SU B: 5.707 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2008	919	5.066 %
R_work	0.1751	17220	-
all	0.176	-	-
obs	-	18139	99.978 %

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 44.855 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.246 Å²	0.123 Å²	0 Å²
2-	-	0.246 Å²	-0 Å²
3-	-	-	-0.799 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→43.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1126	0	17	87	1230

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	1177
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1181
X-RAY DIFFRACTION	r_angle_refined_deg	1.422	1.645	1583
X-RAY DIFFRACTION	r_angle_other_deg	0.483	1.567	2707
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.366	5	152
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.277	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.802	10	218
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.721	10	55
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	182
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1412
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	272
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	288
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	1143
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	594
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	685
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.268	0.2	72
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.163	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.268	0.2	19
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.069	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	4.42	2.662	587
X-RAY DIFFRACTION	r_mcbond_other	4.417	2.662	588
X-RAY DIFFRACTION	r_mcangle_it	6.126	4.741	734
X-RAY DIFFRACTION	r_mcangle_other	6.142	4.749	735
X-RAY DIFFRACTION	r_scbond_it	7.153	3.436	590
X-RAY DIFFRACTION	r_scbond_other	7.157	3.441	589
X-RAY DIFFRACTION	r_scangle_it	9.73	5.928	845
X-RAY DIFFRACTION	r_scangle_other	9.724	5.926	846
X-RAY DIFFRACTION	r_lrange_it	10.835	34.847	5162
X-RAY DIFFRACTION	r_lrange_other	10.834	34.083	5109

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.85-1.898	0.273	53	0.261	1276	X-RAY DIFFRACTION	100
1.898-1.95	0.278	81	0.234	1209	X-RAY DIFFRACTION	100
1.95-2.006	0.208	69	0.205	1175	X-RAY DIFFRACTION	100
2.006-2.068	0.244	60	0.206	1152	X-RAY DIFFRACTION	100
2.068-2.136	0.271	51	0.201	1103	X-RAY DIFFRACTION	100
2.136-2.21	0.225	63	0.178	1076	X-RAY DIFFRACTION	100
2.21-2.294	0.218	56	0.179	1052	X-RAY DIFFRACTION	100
2.294-2.387	0.252	61	0.167	998	X-RAY DIFFRACTION	100
2.387-2.493	0.213	57	0.167	966	X-RAY DIFFRACTION	100
2.493-2.614	0.226	40	0.177	943	X-RAY DIFFRACTION	100
2.614-2.755	0.22	59	0.182	867	X-RAY DIFFRACTION	100
2.755-2.921	0.22	45	0.202	848	X-RAY DIFFRACTION	100
2.921-3.122	0.285	35	0.225	820	X-RAY DIFFRACTION	100
3.122-3.371	0.237	38	0.202	732	X-RAY DIFFRACTION	100
3.371-3.691	0.176	39	0.163	684	X-RAY DIFFRACTION	100
3.691-4.123	0.115	36	0.139	631	X-RAY DIFFRACTION	100
4.123-4.754	0.147	22	0.121	564	X-RAY DIFFRACTION	100
4.754-5.806	0.147	22	0.157	489	X-RAY DIFFRACTION	100
5.806-8.142	0.218	22	0.177	395	X-RAY DIFFRACTION	100
8.142-43.72	0.191	10	0.186	240	X-RAY DIFFRACTION	98.8142

Refinement TLS params.

Method: refined / Origin x: 7.495 Å / Origin y: 18.064 Å / Origin z: -13.633 Å

	11	12	13	21	22	23	31	32	33
T	0.0392 Å²	-0.0048 Å²	0.0288 Å²	-	0.1837 Å²	-0.0175 Å²	-	-	0.044 Å²
L	6.309 °²	-0.8823 °²	1.0815 °²	-	1.6509 °²	-0.4273 °²	-	-	2.6747 °²
S	-0.1068 Å °	0.1898 Å °	-0.3998 Å °	0.0153 Å °	0.0532 Å °	0.1148 Å °	0.2527 Å °	-0.1347 Å °	0.0536 Å °

Refinement TLS group

Selection: ALL

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