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- PDB-7uqv: Pseudobacteroides cellulosolvens pseudo-CphB -

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Basic information

Entry
Database: PDB / ID: 7uqv
TitlePseudobacteroides cellulosolvens pseudo-CphB
ComponentsCyanophycinase
KeywordsHYDROLASE / Cyanophycinase / cyanophycin / protease
Function / homology
Function and homology information


cyanophycinase / : / carboxypeptidase activity / serine-type peptidase activity / proteolysis
Similarity search - Function
Peptidase S51, cyanophycinase / Peptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Biological speciesPseudobacteroides cellulosolvens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSharon, I. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)178084 Canada
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2022
Title: The structure of cyanophycinase in complex with a cyanophycin degradation intermediate.
Authors: Sharon, I. / Grogg, M. / Hilvert, D. / Schmeing, T.M.
History
DepositionApr 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanophycinase
B: Cyanophycinase
D: Cyanophycinase
C: Cyanophycinase


Theoretical massNumber of molelcules
Total (without water)119,8284
Polymers119,8284
Non-polymers00
Water0
1
A: Cyanophycinase
B: Cyanophycinase


Theoretical massNumber of molelcules
Total (without water)59,9142
Polymers59,9142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cyanophycinase
C: Cyanophycinase


Theoretical massNumber of molelcules
Total (without water)59,9142
Polymers59,9142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.797, 172.797, 116.938
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 18 or resid 20...
d_2ens_1(chain "B" and (resid 7 through 18 or resid 20...
d_3ens_1(chain "C" and (resid 7 through 18 or resid 20...
d_4ens_1(chain "D" and (resid 7 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYLYSA1 - 12
d_12ens_1GLYGLYA14 - 29
d_13ens_1GLUVALA32 - 44
d_14ens_1VALILEA46 - 112
d_15ens_1ALAASPA114 - 138
d_16ens_1PROGLNA141 - 167
d_17ens_1GLYSERA169 - 225
d_18ens_1LEULEUA227 - 257
d_21ens_1GLYLYSB1 - 12
d_22ens_1GLYGLYB14 - 29
d_23ens_1GLUVALB32 - 44
d_24ens_1VALILEB46 - 112
d_25ens_1ALAASPB114 - 138
d_26ens_1PROGLNB141 - 167
d_27ens_1GLYSERB169 - 225
d_28ens_1LEULEUB227 - 257
d_31ens_1GLYLYSD1 - 12
d_32ens_1GLYGLYD14 - 29
d_33ens_1GLUVALD32 - 44
d_34ens_1VALILED46 - 112
d_35ens_1ALAASPD114 - 138
d_36ens_1PROGLND142 - 168
d_37ens_1GLYSERD170 - 226
d_38ens_1LEULEUD228 - 258
d_41ens_1GLYLYSC1 - 12
d_42ens_1GLYGLYC14 - 29
d_43ens_1GLUVALC32 - 44
d_44ens_1VALILEC46 - 112
d_45ens_1ALAASPC114 - 138
d_46ens_1PROGLNC142 - 168
d_47ens_1GLYSERC170 - 226
d_48ens_1LEULEUC228 - 258

NCS oper:
IDCodeMatrixVector
1given(-0.81503144776, -0.100317574307, 0.570666385419), (-0.104883303817, -0.943084557026, -0.315580434882), (0.569844919028, -0.317061354607, 0.758121933249)-150.056773671, 2.90187460555, 49.1663601254
2given(-0.736061555261, -0.133256268418, -0.663668707862), (-0.176629198597, -0.908657706885, 0.378342831201), (-0.653464240085, 0.395706884759, 0.645291057031)-120.821748037, 33.9130808086, -56.9953201135
3given(0.254000608244, 0.430343950012, -0.866191535227), (0.459944859298, 0.734077824803, 0.499580297387), (0.850843356569, -0.525294043198, -0.0114782735396)-42.2346949255, 76.5894031704, 73.2674073975

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Components

#1: Protein
Cyanophycinase / / pseudo-CphB


Mass: 29957.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudobacteroides cellulosolvens (bacteria)
Strain: ATCC 35603 = DSM 2933 / Gene: Bccel_3994 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0L6JSP1, cyanophycinase

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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: 4.21 Å3/Da / Density % sol: 70.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.3 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.522 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.522 Å / Relative weight: 1
ReflectionResolution: 2.4→149.65 Å / Num. obs: 76986 / % possible obs: 97.81 % / Redundancy: 18.1 % / Biso Wilson estimate: 62.2 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.96
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 6145 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158_finalrefinement
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EN0

3en0


Resolution: 2.4→92.14 Å / SU ML: 0.4248 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8455
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 3863 5.02 %
Rwork0.2003 73123 -
obs0.2018 76986 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.1 Å2
Refinement stepCycle: LAST / Resolution: 2.4→92.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7864 0 0 0 7864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747964
X-RAY DIFFRACTIONf_angle_d1.129910752
X-RAY DIFFRACTIONf_chiral_restr0.06511259
X-RAY DIFFRACTIONf_plane_restr0.00711401
X-RAY DIFFRACTIONf_dihedral_angle_d11.26282928
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.408563280349
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.499151947676
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.532035202772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.39351050.39241681X-RAY DIFFRACTION64.87
2.43-2.460.41241200.3762207X-RAY DIFFRACTION83.71
2.46-2.490.42441250.36872418X-RAY DIFFRACTION91.44
2.49-2.530.3911560.36342602X-RAY DIFFRACTION99.32
2.53-2.560.38761750.35282604X-RAY DIFFRACTION99.89
2.56-2.60.34781380.32562645X-RAY DIFFRACTION99.96
2.6-2.640.33681400.31682686X-RAY DIFFRACTION100
2.64-2.680.30951450.31022602X-RAY DIFFRACTION99.96
2.68-2.730.30281490.28532657X-RAY DIFFRACTION99.96
2.73-2.780.29261510.28392668X-RAY DIFFRACTION99.96
2.78-2.830.32211360.26542639X-RAY DIFFRACTION100
2.83-2.890.25631680.26822621X-RAY DIFFRACTION100
2.89-2.950.27891230.25732679X-RAY DIFFRACTION100
2.96-3.020.28221540.25352654X-RAY DIFFRACTION100
3.02-3.10.26211210.24212665X-RAY DIFFRACTION99.96
3.1-3.180.31811110.22782689X-RAY DIFFRACTION100
3.18-3.280.281640.23192643X-RAY DIFFRACTION100
3.28-3.380.25761410.22852655X-RAY DIFFRACTION100
3.38-3.50.26281300.21982677X-RAY DIFFRACTION99.96
3.5-3.640.19491350.18772673X-RAY DIFFRACTION100
3.64-3.810.22031310.18362691X-RAY DIFFRACTION100
3.81-4.010.20161260.17272716X-RAY DIFFRACTION99.93
4.01-4.260.181220.15692686X-RAY DIFFRACTION100
4.26-4.590.16471470.14372672X-RAY DIFFRACTION99.93
4.59-5.050.14681540.14062689X-RAY DIFFRACTION99.96
5.05-5.780.24921470.18092717X-RAY DIFFRACTION99.97
5.78-7.290.19941460.19292737X-RAY DIFFRACTION100
7.29-92.140.20641030.15692850X-RAY DIFFRACTION99.13

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