PDB-7pjo: Crystal form 3 of CPR-C4: a cysteine protease from the Candidate ...

ID or keywords:

Entry

Database: PDB / ID: 7pjo

Title

Crystal form 3 of CPR-C4: a cysteine protease from the Candidate Phyla Radiation

Components

CPR-C4

Keywords

HYDROLASE / cysteine protease

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Candidate division CPR1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.248 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	Aug 24, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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	7pjo.cif.gz	188 KB	Display	PDBx/mmCIF format
PDB format	pdb7pjo.ent.gz		Display	PDB format
PDBx/mmJSON format	7pjo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7pjo_validation.pdf.gz	441.1 KB	Display	wwPDB validaton report
Full document	7pjo_full_validation.pdf.gz	442.7 KB	Display
Data in XML	7pjo_validation.xml.gz	18.7 KB	Display
Data in CIF	7pjo_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pj/7pjo ftp://data.pdbj.org/pub/pdb/validation_reports/pj/7pjo	HTTPS FTP

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Related structure data

Related structure data	7ob6SC 7ob7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: CPR-C4

BBB: CPR-C4

hetero molecules

55 kDa, 2 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)	44.780, 77.545, 161.722
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	AAA	11 - 230
2	2	1	BBB	11 - 230

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	CPR-C4 Mass: 27331.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidate division CPR1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.57 Å³/Da / Density % sol: 52.11 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / Details: Lithium sulfate, Tris, PEG4000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 27, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.248→44.302 Å / Num. obs: 27119 / % possible obs: 98.1 % / Redundancy: 12.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.085 / R_pim(I) all: 0.035 / R_rim(I) all: 0.092 / Net I/σ(I): 17.1

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
8.99-44.26	11.4	0.033	5727	0.999	0.013	0.035
2.25-2.32	8.1	1.77	16676	0.36	0.905	1.998

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Aimless	0.7.7	data scaling
XDS		data reduction
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7OB6

7ob6

Resolution: 2.248→44.26 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.948 / SU B: 6.2 / SU ML: 0.149 / Cross valid method: FREE R-VALUE / ESU R: 0.24 / ESU R Free: 0.196
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2246	1323	4.889 %
R_work	0.1788	25740	-
all	0.181	-	-
obs	-	27063	97.866 %

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: 57.088 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.058 Å²	-0 Å²	0 Å²
2-	-	0.085 Å²	-0 Å²
3-	-	-	-0.027 Å²

Refinement step

Cycle: LAST / Resolution: 2.248→44.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3493	0	20	181	3694

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	3614
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3393
X-RAY DIFFRACTION	r_angle_refined_deg	1.442	1.642	4892
X-RAY DIFFRACTION	r_angle_other_deg	1.226	1.587	7827
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.428	5	431
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.929	21.808	177
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.927	15	640
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.341	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	462
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3965
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	815
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	666
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	2852
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	1663
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1607
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.228	0.2	169
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.185	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	4.543	5.808	1733
X-RAY DIFFRACTION	r_mcbond_other	4.541	5.806	1732
X-RAY DIFFRACTION	r_mcangle_it	6.122	8.689	2161
X-RAY DIFFRACTION	r_mcangle_other	6.121	8.692	2162
X-RAY DIFFRACTION	r_scbond_it	5.575	6.344	1881
X-RAY DIFFRACTION	r_scbond_other	5.462	6.312	1866
X-RAY DIFFRACTION	r_scangle_it	8.1	9.267	2731
X-RAY DIFFRACTION	r_scangle_other	8.062	9.22	2707
X-RAY DIFFRACTION	r_lrange_it	9.462	65.502	4009
X-RAY DIFFRACTION	r_lrange_other	9.48	65.211	3965
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.08	0.05	6903

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.07959	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.07959	0.05009

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 (%)
2.248-2.306	0.305	68	0.301	1555	X-RAY DIFFRACTION	82.1356
2.306-2.369	0.327	78	0.292	1689	X-RAY DIFFRACTION	89.3778
2.369-2.438	0.24	96	0.25	1763	X-RAY DIFFRACTION	98.883
2.438-2.513	0.25	89	0.222	1776	X-RAY DIFFRACTION	100
2.513-2.595	0.289	90	0.209	1713	X-RAY DIFFRACTION	100
2.595-2.686	0.27	75	0.179	1658	X-RAY DIFFRACTION	100
2.686-2.788	0.267	98	0.182	1606	X-RAY DIFFRACTION	100
2.788-2.901	0.229	79	0.175	1532	X-RAY DIFFRACTION	100
2.901-3.03	0.255	79	0.171	1477	X-RAY DIFFRACTION	100
3.03-3.178	0.172	61	0.155	1447	X-RAY DIFFRACTION	100
3.178-3.35	0.249	62	0.184	1352	X-RAY DIFFRACTION	100
3.35-3.553	0.229	69	0.189	1295	X-RAY DIFFRACTION	100
3.553-3.798	0.202	55	0.171	1224	X-RAY DIFFRACTION	100
3.798-4.103	0.202	66	0.153	1151	X-RAY DIFFRACTION	100
4.103-4.494	0.178	63	0.156	1034	X-RAY DIFFRACTION	100
4.494-5.024	0.172	56	0.14	956	X-RAY DIFFRACTION	100
5.024-5.8	0.235	47	0.171	841	X-RAY DIFFRACTION	100
5.8-7.101	0.266	46	0.186	728	X-RAY DIFFRACTION	100
7.101-10.033	0.197	32	0.163	590	X-RAY DIFFRACTION	100
10.033-44.26	0.416	14	0.263	353	X-RAY DIFFRACTION	98.3914

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