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- PDB-8eip: Crystal structure of cyanophycin dipeptide hydrolase CphZ E251A f... -

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Basic information

Entry
Database: PDB / ID: 8eip
TitleCrystal structure of cyanophycin dipeptide hydrolase CphZ E251A from Acinetobacter baylyi DSM587 in complex with beta-Asp-Arg
ComponentsSuccinylglutamate desuccinylase
KeywordsHYDROLASE / CphZ / cyanophycin
Function / homologySuccinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / hydrolase activity, acting on ester bonds / metal ion binding / Chem-7ID / : / Succinylglutamate desuccinylase/aspartoacylase
Function and homology information
Biological speciesAcinetobacter baylyi ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsSharon, I. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Discovery of cyanophycin dipeptide hydrolase enzymes suggests widespread utility of the natural biopolymer cyanophycin.
Authors: Sharon, I. / McKay, G.A. / Nguyen, D. / Schmeing, T.M.
History
DepositionSep 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinylglutamate desuccinylase
B: Succinylglutamate desuccinylase
C: Succinylglutamate desuccinylase
D: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,30916
Polymers164,6704
Non-polymers1,63912
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-40 kcal/mol
Surface area29000 Å2
MethodPISA
2
C: Succinylglutamate desuccinylase
D: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1548
Polymers82,3352
Non-polymers8196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-40 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.529, 126.648, 109.516
Angle α, β, γ (deg.)90.00, 130.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-594-

HOH

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Components

#1: Protein
Succinylglutamate desuccinylase


Mass: 41167.598 Da / Num. of mol.: 4 / Mutation: E251A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi ADP1 (bacteria) / Strain: ATCC 33305 / BD413 / ADP1 / Gene: ACIAD1282 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FCQ4
#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.: 4 / Source method: obtained synthetically / Formula: C10H19N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M bis-tris propane pH 7.5, 24% PEG3350, 0.2 M NaBr, 10 mM spermine and 10 mM LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.24→85.6 Å / Num. obs: 73553 / % possible obs: 99.3 % / Redundancy: 2.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07169 / Net I/σ(I): 6.68
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6064 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model generated using Rosetta

Resolution: 2.24→49.04 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 3641 4.97 %RANDOM
Rwork0.2259 ---
obs0.2275 73247 96.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11424 0 88 437 11949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.583
X-RAY DIFFRACTIONf_dihedral_angle_d11.9144399
X-RAY DIFFRACTIONf_chiral_restr0.081778
X-RAY DIFFRACTIONf_plane_restr0.0082142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.270.35411060.33892069X-RAY DIFFRACTION75
2.27-2.30.34091090.33462165X-RAY DIFFRACTION79
2.3-2.330.3481230.30192353X-RAY DIFFRACTION86
2.33-2.370.32891360.29822625X-RAY DIFFRACTION96
2.37-2.410.33831520.30922744X-RAY DIFFRACTION99
2.41-2.440.32681530.30962703X-RAY DIFFRACTION99
2.44-2.490.35211480.3162734X-RAY DIFFRACTION100
2.49-2.530.35521350.30562798X-RAY DIFFRACTION100
2.53-2.580.31891490.30512705X-RAY DIFFRACTION100
2.58-2.630.36171500.30972741X-RAY DIFFRACTION100
2.63-2.690.40441500.30712769X-RAY DIFFRACTION100
2.69-2.750.3661470.30732728X-RAY DIFFRACTION99
2.75-2.820.31341340.30012751X-RAY DIFFRACTION100
2.82-2.90.29671490.28522745X-RAY DIFFRACTION100
2.9-2.980.34991390.27472763X-RAY DIFFRACTION100
2.98-3.080.28991360.27122741X-RAY DIFFRACTION100
3.08-3.190.2931280.26982775X-RAY DIFFRACTION99
3.19-3.320.29411300.25492707X-RAY DIFFRACTION99
3.32-3.470.27221240.23062750X-RAY DIFFRACTION99
3.47-3.650.26151510.21732737X-RAY DIFFRACTION98
3.65-3.880.24021470.21092725X-RAY DIFFRACTION99
3.88-4.180.23631420.19712744X-RAY DIFFRACTION99
4.18-4.60.21471520.17732703X-RAY DIFFRACTION98
4.6-5.260.20941400.17632767X-RAY DIFFRACTION99
5.27-6.630.25511340.19932772X-RAY DIFFRACTION99
6.63-49.040.17481770.16612792X-RAY DIFFRACTION100

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