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- PDB-6t26: X-ray crystal structure of Vibrio alkaline phosphatase with the n... -

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Basic information

Entry
Database: PDB / ID: 6t26
TitleX-ray crystal structure of Vibrio alkaline phosphatase with the non-competitive inhibitor cyclohexylamine
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / Enzyme dynamics Disordered loop Homodimer / non-competative inhibition.
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
CYCLOHEXYLAMMONIUM ION / PHOSPHATE ION / Alkaline phosphatase
Similarity search - Component
Biological speciesVibrio sp. G15-21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.265 Å
AuthorsAsgeirsson, B. / Hjorleifsson, J.G. / Markusson, S. / Helland, R.
Funding support Iceland, 2items
OrganizationGrant numberCountry
Other government141619-051 Iceland
Other government196071-00911 Iceland
CitationJournal: Biochem Biophys Rep / Year: 2020
Title: X-ray crystal structure of Vibrio alkaline phosphatase with the non-competitive inhibitor cyclohexylamine.
Authors: Asgeirsson, B. / Markusson, S. / Hlynsdottir, S.S. / Helland, R. / Hjorleifsson, J.G.
History
DepositionOct 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)114,46324
Polymers113,2522
Non-polymers1,21122
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, doi: 10.1002/2211-5463.12565 doi: 10.1016/j.bbapap.2016.03.016, homology, assay for oligomerization, doi: 10.1002/2211-5463.12565
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-329 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.916, 85.270, 84.785
Angle α, β, γ (deg.)90.000, 113.550, 90.000
Int Tables number4
Space group name H-MP1211

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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: Contains C-terminal StrepTagII / Source: (gene. exp.) Vibrio sp. G15-21 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q93P54

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Non-polymers , 6 types, 433 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-HAI / CYCLOHEXYLAMMONIUM ION


Mass: 100.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14N / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 45.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 mg/mL Protein, 200 mM cyclohexylamine pH 8.0, 0.5 M NaCl, 22% (w/v) PEG3350 0.1 M Tris pH 7.0.
Temp details: In incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 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: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.26→29.43 Å / Num. obs: 46452 / % possible obs: 99 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.042 / Rrim(I) all: 0.109 / Net I/σ(I): 13 / Num. measured all: 315308 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.26-2.326.50.7221976330620.810.3030.7842.388.4
10.13-29.4360.04632075360.9950.020.05138.295.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472: ???refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E2D

3e2d


Resolution: 2.265→28.721 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 2017 4.35 %RANDOM
Rwork0.1604 44401 --
obs0.1623 46418 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.64 Å2 / Biso mean: 40.6475 Å2 / Biso min: 25.1 Å2
Refinement stepCycle: final / Resolution: 2.265→28.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 54 411 8265
Biso mean--40.42 41.4 -
Num. residues----1004
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.265-2.32170.24831300.1943282289
2.3217-2.38440.24771470.19633163100
2.3844-2.45450.27921420.19473189100
2.4545-2.53370.2631560.1983164100
2.5337-2.62420.2611380.19263184100
2.6242-2.72920.24881370.18163203100
2.7292-2.85330.24631530.18193191100
2.8533-3.00360.2341360.18423180100
3.0036-3.19160.23491460.1793208100
3.1916-3.43760.18931440.17013179100
3.4376-3.78290.19331510.14963200100
3.7829-4.32860.17841360.13493226100
4.3286-5.44750.16721490.13163220100
5.4475-28.7210.18341520.14743272100

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