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- PDB-7qp8: Crystal structure of Vibrio alkaline phosphatase with bound HEPES -

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Basic information

Entry
Database: PDB / ID: 7qp8
TitleCrystal structure of Vibrio alkaline phosphatase with bound HEPES
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / Phosphatase / HEPES
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: 1.7 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
DepositionJan 3, 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)120,65823
Polymers117,2332
Non-polymers3,42521
Water14,970831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, homology, assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13110 Å2
ΔGint-272 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.810, 85.050, 85.500
Angle α, β, γ (deg.)90.000, 113.904, 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, 852 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.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / 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: 1.51 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 23% PEG3350, 0.4 M NaCl and 0.1 M HEPES pH 7.5, 10 mg/mL protein. Crystal dehydrated in the mother liquior with PEG3350 increased to 30% prior to data collection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→44.1 Å / Num. obs: 517701 / % possible obs: 79.6 % / Redundancy: 5.88 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0092 / Net I/σ(I): 12.14
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 0.76 / Num. unique obs: 7929 / CC1/2: 0.375 / Rrim(I) all: 1.671 / % possible all: 29.9

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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: 1.7→44.1 Å / SU ML: 0.1799 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1812 2015 2.29 %
Rwork0.1503 85986 -
obs0.151 88001 79.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.6 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7804 0 120 831 8755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00368239
X-RAY DIFFRACTIONf_angle_d0.654111151
X-RAY DIFFRACTIONf_chiral_restr0.04111189
X-RAY DIFFRACTIONf_plane_restr0.00371462
X-RAY DIFFRACTIONf_dihedral_angle_d14.84623146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.4122510.36222289X-RAY DIFFRACTION29.75
1.74-1.790.2915700.31642900X-RAY DIFFRACTION38.1
1.79-1.840.3014820.28473641X-RAY DIFFRACTION47.4
1.84-1.90.2951050.24384432X-RAY DIFFRACTION57.68
1.9-1.970.24781340.21155278X-RAY DIFFRACTION68.68
1.97-2.050.24851440.18376273X-RAY DIFFRACTION81.69
2.05-2.140.20661600.15977077X-RAY DIFFRACTION91.84
2.14-2.250.19511780.14467645X-RAY DIFFRACTION99.59
2.25-2.40.17121810.13927707X-RAY DIFFRACTION99.95
2.4-2.580.16451800.1437704X-RAY DIFFRACTION99.97
2.58-2.840.17811820.157708X-RAY DIFFRACTION99.94
2.84-3.250.20841800.15497740X-RAY DIFFRACTION99.97
3.25-4.10.15831810.1317751X-RAY DIFFRACTION99.97
4.1-44.10.15251870.13647841X-RAY DIFFRACTION99.76

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