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- PDB-7yzz: Crystal structure of Vibrio alkaline phosphatase in 0.5 M NaCl -

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Basic information

Entry
Database: PDB / ID: 7yzz
TitleCrystal structure of Vibrio alkaline phosphatase in 0.5 M NaCl
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / Phosphatase / Chloride
Function / homology
Function and homology information


alkaline phosphatase activity / metal ion binding
Similarity search - Function
Alkaline phosphatase, crown domain / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Alkaline phosphatase
Similarity search - Component
Biological speciesVibrio sp. G15-21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsMarkusson, S. / Hjorleifsson, J.G. / Kursula, P. / Asgeirsson, B.
Funding support Iceland, 1items
OrganizationGrant numberCountry
Other government141619053 Iceland
CitationJournal: Biochemistry / Year: 2022
Title: Structural Characterization of Functionally Important Chloride Binding Sites in the Marine Vibrio Alkaline Phosphatase.
Authors: Markusson, S. / Hjorleifsson, J.G. / Kursula, P. / Asgeirsson, B.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Alkaline phosphatase
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,57926
Polymers113,2522
Non-polymers1,32724
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, assay for oligomerization, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-260 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.080, 84.740, 85.230
Angle α, β, γ (deg.)90.000, 113.480, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alkaline phosphatase


Mass: 56626.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Submitted sequence contains the C-terminal StrepTag-II included in the crystallised construct, but was not built into the model due to lack of electron density
Source: (gene. exp.) Vibrio sp. G15-21 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: Q93P54

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Non-polymers , 6 types, 791 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Vibrio sp. G15-21 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 26% PEG3350, 0.5 M NaCl, 1.0 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.29→39.31 Å / Num. obs: 1574856 / % possible obs: 96.8 % / Redundancy: 6.45 % / Biso Wilson estimate: 16.87 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.057 / Net I/σ(I): 15.32
Reflection shellResolution: 1.29→1.32 Å / Num. unique obs: 53734 / CC1/2: 0.584

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Processing

Software
NameVersionClassification
PHENIXdev_3958refinement
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E2D

3e2d


Resolution: 1.29→39.31 Å / SU ML: 0.1058 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1387 1994 0.82 %
Rwork0.1209 241974 -
obs0.121 243968 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 1.29→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7799 0 65 767 8631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00988146
X-RAY DIFFRACTIONf_angle_d1.105711015
X-RAY DIFFRACTIONf_chiral_restr0.08121186
X-RAY DIFFRACTIONf_plane_restr0.00891459
X-RAY DIFFRACTIONf_dihedral_angle_d14.04473025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.320.2851040.293313853X-RAY DIFFRACTION77.89
1.32-1.360.30091350.245116102X-RAY DIFFRACTION90.46
1.36-1.40.21500.190817523X-RAY DIFFRACTION98.34
1.4-1.440.20641420.154917577X-RAY DIFFRACTION99.06
1.44-1.490.17131440.130617687X-RAY DIFFRACTION99.4
1.49-1.550.14341450.11117712X-RAY DIFFRACTION99.39
1.55-1.630.13941490.103417525X-RAY DIFFRACTION98.5
1.63-1.710.12771390.097817602X-RAY DIFFRACTION98.56
1.71-1.820.13991540.093617712X-RAY DIFFRACTION99.4
1.82-1.960.12121410.093217780X-RAY DIFFRACTION99.71
1.96-2.160.12981480.097217729X-RAY DIFFRACTION99.27
2.16-2.470.13611460.10117511X-RAY DIFFRACTION97.93
2.47-3.110.13751520.119917825X-RAY DIFFRACTION99.44
3.11-39.310.12611450.131717836X-RAY DIFFRACTION98.31

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