PDB-7ob7: CPR-C4 - novel protease from the Candidate Phyla Radiation (CPR)

ID or keywords:

Entry

Database: PDB / ID: 7ob7

Title

CPR-C4 - novel protease from the Candidate Phyla Radiation (CPR)

Components

CPR-C4

Keywords

HYDROLASE / cysteine protease / peptidase

Biological species

candidate division CPR1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.682 Å

Authors

Cornish, K.A.S. / Pohl, E.

Funding support

European Union, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins.
Authors: Cornish, K.A.S. / Lange, J. / Aevarsson, A. / Pohl, E.

History

Deposition	Apr 21, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 27, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 25, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ob7.cif.gz	58.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7ob7.ent.gz	38.7 KB	Display	PDB format
PDBx/mmJSON format	7ob7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ob7_validation.pdf.gz	426.7 KB	Display	wwPDB validaton report
Full document	7ob7_full_validation.pdf.gz	426.7 KB	Display
Data in XML	7ob7_validation.xml.gz	9.3 KB	Display
Data in CIF	7ob7_validation.cif.gz	11.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ob/7ob7 ftp://data.pdbj.org/pub/pdb/validation_reports/ob/7ob7	HTTPS FTP

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Related structure data

Related structure data	7ob6SC 7pjoC S: Starting model for refinement C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CPR-C4

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

1

A: CPR-C4

defined by author&software
54.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.307, 79.731, 126.196
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

#1: Protein	CPR-C4 Mass: 27174.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) candidate division CPR1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium malonate dibasic monohydrate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 1.2819 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.2819 Å / Relative weight: 1

Reflection

Resolution: 2.581→67.405 Å / Num. obs: 9190 / % possible obs: 98.9 % / Redundancy: 9.7 % / CC_1/2: 0.968 / R_merge(I) obs: 0.505 / R_pim(I) all: 0.243 / R_rim(I) all: 0.562 / Net I/σ(I): 6.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.93-67.4	8.4	0.133	260	0.986	0.068	0.15
2.581-2.69	8.2	7.895	1015	0.181	3.982	8.889

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
Aimless		data scaling
DIALS		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7OB6

7ob6

Resolution: 2.682→67.405 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.914 / SU B: 17.409 / SU ML: 0.324 / Cross valid method: FREE R-VALUE / ESU R: 0.789 / ESU R Free: 0.318 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2506	398	4.858 %
R_work	0.2348	7795	-
all	0.236	-	-
obs	-	8193	98.747 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 49.032 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.94 Å²	-0 Å²	-0 Å²
2-	-	6.08 Å²	0 Å²
3-	-	-	-4.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.682→67.405 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1653	0	0	18	1671

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	1700
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.223	0.1	27272
X-RAY DIFFRACTION	r_angle_refined_deg	1.406	1.632	2317
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.331	5	209
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.876	22	80
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.335	15	266
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.829	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	227
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1286
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	663
X-RAY DIFFRACTION	r_nbtor_refined	0.296	0.2	1153
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.128	0.2	35
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.304	0.2	31
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.194	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.833	4.894	842
X-RAY DIFFRACTION	r_mcangle_it	5.989	7.33	1049
X-RAY DIFFRACTION	r_scbond_it	5.74	5.308	858
X-RAY DIFFRACTION	r_scangle_it	8.816	7.776	1268
X-RAY DIFFRACTION	r_lrange_it	14.438	188.929	27361

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.682-2.751	0.408	33	0.39	515	0.391	621	0.253	0.33	88.2448	0.353
2.751-2.827	0.375	24	0.369	534	0.369	560	0.454	0.477	99.6429	0.318
2.827-2.908	0.346	29	0.325	534	0.326	563	0.548	0.588	100	0.291
2.908-2.998	0.331	26	0.319	532	0.319	558	0.682	0.711	100	0.295
2.998-3.096	0.337	27	0.28	505	0.283	533	0.815	0.812	99.8124	0.246
3.096-3.204	0.328	29	0.254	492	0.258	522	0.835	0.848	99.8084	0.222
3.204-3.325	0.239	37	0.228	487	0.229	524	0.877	0.895	100	0.2
3.325-3.46	0.297	20	0.217	466	0.22	488	0.886	0.902	99.5902	0.183
3.46-3.614	0.173	19	0.2	431	0.199	451	0.952	0.93	99.7783	0.177
3.614-3.79	0.211	17	0.175	431	0.177	448	0.938	0.952	100	0.152
3.79-3.994	0.195	22	0.171	406	0.173	432	0.952	0.954	99.0741	0.16
3.994-4.235	0.18	24	0.169	369	0.17	399	0.955	0.953	98.4962	0.154
4.235-4.527	0.204	19	0.179	356	0.18	375	0.96	0.948	100	0.165
4.527-4.887	0.212	22	0.196	338	0.197	366	0.931	0.947	98.3607	0.184
4.887-5.351	0.301	8	0.208	325	0.21	336	0.914	0.938	99.1071	0.198
5.351-5.978	0.204	10	0.243	286	0.241	298	0.931	0.941	99.3289	0.234
5.978-6.894	0.21	8	0.268	263	0.266	271	0.947	0.926	100	0.259
6.894-8.421	0.216	11	0.195	226	0.196	237	0.96	0.958	100	0.2
8.421-11.817	0.276	6	0.204	184	0.206	191	0.966	0.975	99.4764	0.229
11.817-67.405	0.339	6	0.403	115	0.4	123	0.92	0.863	98.374	0.422

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