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- PDB-7qow: Crystal structure of Vibrio alkaline phosphatase in 1.0 M NaCl -

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Basic information

Entry
Database: PDB / ID: 7qow
TitleCrystal structure of Vibrio alkaline phosphatase in 1.0 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: 1.2 Å
AuthorsMarkusson, S. / Hjorleifsson, J.G. / Kursula, P. / Asgeirsson, B.
Funding support1items
OrganizationGrant numberCountry
Other government141619053
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
DepositionDec 29, 2021Deposition 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
A: Alkaline phosphatase
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,75528
Polymers117,2332
Non-polymers1,52226
Water20,1771120
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 area13440 Å2
ΔGint-262 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.202, 85.993, 85.139
Angle α, β, γ (deg.)90.000, 113.374, 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: 58616.484 Da / Num. of mol.: 2
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 , 7 types, 1146 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1120 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG3350, 1.0 M NaCl, 0.1 M Tris pH 7.0. Grown from seed crystals grown in 28% PEG3350, 0.8 M NaCl, 0.1 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, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.2→43 Å / Num. obs: 1999077 / % possible obs: 95.9 % / Redundancy: 6.55 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 1 / Rrim(I) all: 0.052 / Net I/σ(I): 17.21
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 4.77 % / Mean I/σ(I) obs: 0.79 / Num. unique obs: 198148 / CC1/2: 0.3 / Rrim(I) all: 1.83 / % possible all: 80.9

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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: 1.2→43 Å / SU ML: 0.1381 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Anisotropic refinement of all atoms, excluding hydrogens.
RfactorNum. reflection% reflectionSelection details
Rfree0.1596 3931 10 %Random selection
Rwork0.1314 593613 --
obs0.1316 597544 95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.06 Å2
Refinement stepCycle: LAST / Resolution: 1.2→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7829 0 77 1120 9026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01048135
X-RAY DIFFRACTIONf_angle_d1.14510986
X-RAY DIFFRACTIONf_chiral_restr0.08391181
X-RAY DIFFRACTIONf_plane_restr0.00991449
X-RAY DIFFRACTIONf_dihedral_angle_d13.86053029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.3791050.348313935X-RAY DIFFRACTION62.42
1.21-1.230.3169970.332815763X-RAY DIFFRACTION70.57
1.23-1.250.2911980.323817839X-RAY DIFFRACTION79.82
1.25-1.260.3451220.30719164X-RAY DIFFRACTION85.88
1.26-1.280.28671470.299920268X-RAY DIFFRACTION90.98
1.28-1.30.28711330.283221371X-RAY DIFFRACTION95.77
1.3-1.320.29541500.272621912X-RAY DIFFRACTION98.55
1.32-1.340.26971500.25622024X-RAY DIFFRACTION98.46
1.34-1.370.28681390.243521955X-RAY DIFFRACTION98.48
1.37-1.390.26331450.227522015X-RAY DIFFRACTION98.62
1.39-1.420.25541450.204122044X-RAY DIFFRACTION98.63
1.42-1.450.22931400.188822080X-RAY DIFFRACTION98.96
1.45-1.480.17181500.170522048X-RAY DIFFRACTION98.86
1.48-1.510.2211440.150122114X-RAY DIFFRACTION98.84
1.51-1.550.18961500.132822107X-RAY DIFFRACTION99.06
1.55-1.590.15061420.122222070X-RAY DIFFRACTION99.07
1.59-1.640.13331460.112322110X-RAY DIFFRACTION98.96
1.64-1.690.13611560.102321961X-RAY DIFFRACTION98.95
1.69-1.750.13071460.106422180X-RAY DIFFRACTION98.68
1.75-1.820.15021370.095222059X-RAY DIFFRACTION99.04
1.82-1.90.10741370.103922102X-RAY DIFFRACTION99.1
1.9-2.010.12241490.094622084X-RAY DIFFRACTION99.02
2.01-2.130.13321560.106922085X-RAY DIFFRACTION99.02
2.13-2.30.16341510.100922137X-RAY DIFFRACTION99.14
2.3-2.530.12691430.11722080X-RAY DIFFRACTION98.97
2.53-2.890.16281550.12122035X-RAY DIFFRACTION98.71
2.89-3.640.15481460.126822028X-RAY DIFFRACTION98.82
3.64-430.14121520.122322043X-RAY DIFFRACTION98.78

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