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- PDB-7ob6: CPR-C4 - a conserved novel protease from the Candidate Phyla Radiation -

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Basic information

Entry
Database: PDB / ID: 7ob6
TitleCPR-C4 - a conserved novel protease from the Candidate Phyla Radiation
ComponentsCPR-C4
KeywordsHYDROLASE / Protease / cysteine protease / Zn
Biological speciescandidate division CPR1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.598 Å
AuthorsCornish, K.A.S. / Pohl, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: 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
DepositionApr 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 19, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CPR-C4
B: CPR-C4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4794
Polymers54,3492
Non-polymers1312
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-75 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.392, 123.392, 96.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-306-

HOH

21B-317-

HOH

31B-318-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TRP / End label comp-ID: TRP / Auth seq-ID: 0 - 214 / Label seq-ID: 12 - 226

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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

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Components

#1: Protein CPR-C4


Mass: 27174.287 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)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Morpheus screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763, 1.2824
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
21.28241
ReflectionResolution: 2.598→48.26 Å / Num. obs: 26494 / % possible obs: 99.8 % / Redundancy: 8.5 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.05 / Rrim(I) all: 0.106 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-48.267.80.01869410.0090.02
2.6-2.718.44.08631430.3682.1984.649

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
pointlessdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.598→46.791 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.209 / SU B: 17.956 / SU ML: 0.332 / Average fsc free: 0.7285 / Average fsc work: 0.7496 / Cross valid method: FREE R-VALUE / ESU R: 0.337 / ESU R Free: 0.278 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2853 1313 4.959 %
Rwork0.2344 25166 -
all0.237 --
obs-26479 99.751 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 102.186 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å21.71 Å20 Å2
2--3.42 Å2-0 Å2
3----11.093 Å2
Refinement stepCycle: LAST / Resolution: 2.598→46.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 2 63 3412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123445
X-RAY DIFFRACTIONr_ext_dist_refined_d0.3230.152047
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6314705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3315431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24821.905168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3931517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022659
X-RAY DIFFRACTIONr_nbd_refined0.2020.21433
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.289
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.25
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1720.21
X-RAY DIFFRACTIONr_mcbond_it8.96410.9581736
X-RAY DIFFRACTIONr_mcangle_it12.64616.4082163
X-RAY DIFFRACTIONr_scbond_it10.56710.8511709
X-RAY DIFFRACTIONr_scangle_it14.19416.2232542
X-RAY DIFFRACTIONr_lrange_it18.869404.32752464
X-RAY DIFFRACTIONr_ncsr_local_group_10.0720.056341
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.072040.05009
12BX-RAY DIFFRACTIONLocal ncs0.072040.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.598-2.6650.4651080.4531821X-RAY DIFFRACTION99.1774
2.665-2.7380.497940.4231775X-RAY DIFFRACTION99.7332
2.738-2.8180.3911020.4031725X-RAY DIFFRACTION99.6183
2.818-2.9040.421000.3831692X-RAY DIFFRACTION99.7773
2.904-2.9990.344800.3491640X-RAY DIFFRACTION99.6524
2.999-3.1050.341680.3091596X-RAY DIFFRACTION99.82
3.105-3.2220.383750.291546X-RAY DIFFRACTION99.8153
3.222-3.3530.349650.2581514X-RAY DIFFRACTION100
3.353-3.5020.283710.2391424X-RAY DIFFRACTION100
3.502-3.6730.308820.2131348X-RAY DIFFRACTION99.9301
3.673-3.8710.243570.21324X-RAY DIFFRACTION100
3.871-4.1060.24630.1831234X-RAY DIFFRACTION100
4.106-4.3890.271600.1811157X-RAY DIFFRACTION99.9179
4.389-4.740.2620.1781087X-RAY DIFFRACTION100
4.74-5.1910.325440.1971003X-RAY DIFFRACTION100
5.191-5.8020.289560.248911X-RAY DIFFRACTION99.8967
5.802-6.6960.268420.247817X-RAY DIFFRACTION100
6.696-8.1930.256460.205686X-RAY DIFFRACTION99.8636
8.193-11.5530.237280.168541X-RAY DIFFRACTION99.6497
11.553-46.7910.197100.275325X-RAY DIFFRACTION95.4416

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