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- PDB-7uqw: PCC6803 Cyanophycinase S132DAP covalently bound to cyanophycin dimer -

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Basic information

Entry
Database: PDB / ID: 7uqw
TitlePCC6803 Cyanophycinase S132DAP covalently bound to cyanophycin dimer
ComponentsCyanophycinase
KeywordsHYDROLASE / cyanophycinase / CphB / cyanophycin
Function / homology
Function and homology information


cyanophycinase / peptidyl-dipeptidase activity / serine-type peptidase activity / protein homodimerization activity / proteolysis
Similarity search - Function
Peptidase S51, cyanophycinase / Peptidase S51 / Peptidase family S51 / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Chem-7ID / FORMAMIDE / Cyanophycinase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

Downloads & links

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Assembly

Deposited unit
A: Cyanophycinase
B: Cyanophycinase
C: Cyanophycinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,49917
Polymers90,3523
Non-polymers2,14714
Water9,710539
1
A: Cyanophycinase
B: Cyanophycinase
hetero molecules

A: Cyanophycinase
B: Cyanophycinase
hetero molecules

C: Cyanophycinase
hetero molecules

C: Cyanophycinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,99934
Polymers180,7046
Non-polymers4,29428
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation2_565-x,-y+1,z+1/21
crystal symmetry operation3_555-x,y,-z+1/21
Buried area12780 Å2
ΔGint-57 kcal/mol
Surface area55940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.463, 132.947, 164.092
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Cyanophycinase


Mass: 30117.398 Da / Num. of mol.: 3
Mutation: S132DAP (diaminopropanoate: a modified amino acid)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: cphB, slr2001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73832, cyanophycinase
#2: Chemical
ChemComp-7ID / (2~{S})-4-[[(2~{S})-5-[[azanyl($l^{4}-azanylidene)methyl]amino]-1-$l^{1}-oxidanyl-1-oxidanylidene-pentan-2-yl]amino]-2-$l^{2}-azanyl-4-oxidanylidene-butanoic acid


Type: L-peptide linking / Mass: 289.288 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H19N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ARF / FORMAMIDE


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH3NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.6, 1.65 M ammonium sulfate and 4% formamide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→61.61 Å / Num. obs: 133142 / % possible obs: 99.92 % / Redundancy: 12.9 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.18
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 13155 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.20.1_4487refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EN0

3en0


Resolution: 1.5→61.61 Å / SU ML: 0.1446 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 17.4545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.199 6567 4.93 %
Rwork0.1812 126573 -
obs0.1821 133140 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→61.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 0 106 539 6651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01586210
X-RAY DIFFRACTIONf_angle_d1.65438376
X-RAY DIFFRACTIONf_chiral_restr0.0928939
X-RAY DIFFRACTIONf_plane_restr0.01161108
X-RAY DIFFRACTIONf_dihedral_angle_d12.78492295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28322090.27024169X-RAY DIFFRACTION99.98
1.52-1.530.26642420.2524192X-RAY DIFFRACTION99.95
1.53-1.550.24672110.23214132X-RAY DIFFRACTION100
1.55-1.570.21831790.21484245X-RAY DIFFRACTION99.91
1.57-1.590.23231990.21184232X-RAY DIFFRACTION99.91
1.59-1.620.22662260.20214136X-RAY DIFFRACTION99.89
1.62-1.640.22582060.19694207X-RAY DIFFRACTION99.82
1.64-1.660.24922040.19884246X-RAY DIFFRACTION99.96
1.66-1.690.21522210.18544141X-RAY DIFFRACTION100
1.69-1.720.19182310.18154164X-RAY DIFFRACTION99.95
1.72-1.750.21052460.1784196X-RAY DIFFRACTION99.98
1.75-1.780.21982290.18434173X-RAY DIFFRACTION99.93
1.78-1.810.19582420.17814172X-RAY DIFFRACTION99.98
1.81-1.850.20052210.17534185X-RAY DIFFRACTION99.93
1.85-1.890.20081970.17574211X-RAY DIFFRACTION99.95
1.89-1.930.19232180.17414209X-RAY DIFFRACTION100
1.93-1.980.17542350.16464159X-RAY DIFFRACTION99.89
1.98-2.040.19912130.16594235X-RAY DIFFRACTION99.91
2.04-2.10.20681720.16674236X-RAY DIFFRACTION99.89
2.1-2.160.19342360.17414197X-RAY DIFFRACTION99.86
2.16-2.240.18512220.16584234X-RAY DIFFRACTION99.75
2.24-2.330.18712240.16644217X-RAY DIFFRACTION99.71
2.33-2.440.18331890.16724239X-RAY DIFFRACTION99.95
2.44-2.560.20332450.17084226X-RAY DIFFRACTION99.91
2.56-2.730.18672140.17834230X-RAY DIFFRACTION99.96
2.73-2.940.21252430.17454249X-RAY DIFFRACTION100
2.94-3.230.1792490.1814229X-RAY DIFFRACTION99.98
3.23-3.70.19762550.17644258X-RAY DIFFRACTION100
3.7-4.660.19181850.17414352X-RAY DIFFRACTION99.82
4.66-61.610.20522040.20354502X-RAY DIFFRACTION99.83

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