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- PDB-7z00: Crystal structure of Vibrio alkaline phosphatase in 1.0 M KBr -

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Basic information

Entry
Database: PDB / ID: 7z00
TitleCrystal structure of Vibrio alkaline phosphatase in 1.0 M KBr
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / Alkaline phosphatase / AP
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
BROMIDE ION / PHOSPHATE ION / Alkaline phosphatase
Similarity search - Component
Biological speciesVibrio sp. G15-21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

Downloads & links

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Assembly

Deposited unit
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9717
Polymers58,6161
Non-polymers3546
Water543
1
B: Alkaline phosphatase
hetero molecules

B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,94214
Polymers117,2332
Non-polymers70912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10200 Å2
ΔGint-219 kcal/mol
Surface area34450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.250, 118.120, 84.400
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

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Protein , 1 types, 1 molecules B

#1: Protein Alkaline phosphatase


Mass: 58616.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 , 5 types, 9 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13.4 mg/mL protein in 24% PEG3350, 1.0 M KBr and 0.1 M Tris pH 7.0. Grown from seed crystals grown in 24% PEG3350, 0.4 M KBr, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.6→48.39 Å / Num. obs: 209590 / % possible obs: 99.8 % / Redundancy: 7.12 % / Biso Wilson estimate: 71.52 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.156 / Net I/σ(I): 7.96
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 7.21 % / Num. unique obs: 15872 / CC1/2: 0.371 / Rrim(I) all: 2.994 / % possible all: 100

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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: 2.6→48.39 Å / SU ML: 0.447 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2913 2919 9.93 %
Rwork0.242 26485 -
obs0.2467 29404 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 10 3 3912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693999
X-RAY DIFFRACTIONf_angle_d0.98785411
X-RAY DIFFRACTIONf_chiral_restr0.0393586
X-RAY DIFFRACTIONf_plane_restr0.0045714
X-RAY DIFFRACTIONf_dihedral_angle_d17.83541477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.42611380.39751270X-RAY DIFFRACTION99.72
2.64-2.690.39491360.36391248X-RAY DIFFRACTION99.93
2.69-2.740.43641410.36831273X-RAY DIFFRACTION99.86
2.74-2.790.37851420.35851260X-RAY DIFFRACTION99.93
2.79-2.850.38521360.35291269X-RAY DIFFRACTION99.93
2.85-2.910.41951380.35251253X-RAY DIFFRACTION100
2.91-2.980.40261370.33681279X-RAY DIFFRACTION99.65
2.98-3.050.42941350.3071225X-RAY DIFFRACTION99.78
3.05-3.130.38471400.32911275X-RAY DIFFRACTION100
3.13-3.230.42281450.29251280X-RAY DIFFRACTION99.86
3.23-3.330.31420.28231276X-RAY DIFFRACTION99.86
3.33-3.450.36171340.28681246X-RAY DIFFRACTION100
3.45-3.590.28141440.27491252X-RAY DIFFRACTION100
3.59-3.750.36641350.28021216X-RAY DIFFRACTION96.36
3.75-3.950.321420.21761288X-RAY DIFFRACTION99.93
3.95-4.190.24661430.22171251X-RAY DIFFRACTION100
4.19-4.520.2331420.1851261X-RAY DIFFRACTION99.57
4.52-4.970.23281400.19271253X-RAY DIFFRACTION99.71
4.97-5.690.2211360.20751276X-RAY DIFFRACTION99.93
5.69-7.160.30151330.22421270X-RAY DIFFRACTION99.93
7.17-48.390.2261400.1991264X-RAY DIFFRACTION99.79

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