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- PDB-8ein: Crystal structure of WT cyanophycin dipeptide hydrolase CphZ from... -

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Basic information

Entry
Database: PDB / ID: 8ein
TitleCrystal structure of WT cyanophycin dipeptide hydrolase CphZ from Acinetobacter baylyi DSM587
ComponentsSuccinylglutamate desuccinylase
KeywordsHYDROLASE / CphZ / cyanophycin
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
: / Succinylglutamate desuccinylase/aspartoacylase / AstE/AspA barrel-sandwich hybrid domain / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Succinylglutamate desuccinylase/aspartoacylase
Similarity search - Component
Biological speciesAcinetobacter baylyi ADP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)165,38412
Polymers164,9034
Non-polymers4818
Water00
1
A: Succinylglutamate desuccinylase
B: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6926
Polymers82,4512
Non-polymers2414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-115 kcal/mol
Surface area29520 Å2
MethodPISA
2
C: Succinylglutamate desuccinylase
D: Succinylglutamate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6926
Polymers82,4512
Non-polymers2414
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-115 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.632, 128.015, 107.078
Angle α, β, γ (deg.)90.00, 129.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Succinylglutamate desuccinylase


Mass: 41225.633 Da / Num. of mol.: 4
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-ZN / ZINC ION


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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.13 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→81.8 Å / Num. obs: 39871 / % possible obs: 83.81 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Net I/σ(I): 15.26
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 1138 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ab initio model generated with Rosetta

Resolution: 2.7→48.94 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 33.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1980 4.97 %RANDOM
Rwork0.2422 ---
obs0.2433 39871 91.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11440 0 8 0 11448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.772
X-RAY DIFFRACTIONf_dihedral_angle_d12.5144367
X-RAY DIFFRACTIONf_chiral_restr0.0881770
X-RAY DIFFRACTIONf_plane_restr0.0072130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.4431440.40082219X-RAY DIFFRACTION76
2.77-2.840.38921460.35522848X-RAY DIFFRACTION97
2.84-2.930.3581460.32462847X-RAY DIFFRACTION96
2.93-3.020.3311360.30992789X-RAY DIFFRACTION95
3.02-3.130.33761460.32092894X-RAY DIFFRACTION98
3.13-3.250.3241350.3262921X-RAY DIFFRACTION98
3.25-3.40.36251330.32915X-RAY DIFFRACTION98
3.4-3.580.29071420.27582906X-RAY DIFFRACTION98
3.58-3.810.29241620.25212872X-RAY DIFFRACTION97
3.81-4.10.29721520.24442759X-RAY DIFFRACTION94
4.1-4.510.25691270.22512468X-RAY DIFFRACTION83
4.51-5.160.21761430.20182480X-RAY DIFFRACTION84
5.16-6.50.24271130.22052588X-RAY DIFFRACTION86
6.5-48.940.18171550.17522385X-RAY DIFFRACTION80

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