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- PDB-5too: Crystal structure of alkaline phosphatase PafA T79S, N100A, K162A... -

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Basic information

Entry
Database: PDB / ID: 5too
TitleCrystal structure of alkaline phosphatase PafA T79S, N100A, K162A, R164A mutant
ComponentsAlkaline phosphatase PafA
KeywordsHYDROLASE / Alkaline Phosphatase / Phosphomonoesterase / PafA / Weak phosphate binder / Zinc bimetallo core
Function / homology
Function and homology information


glucose-6-phosphatase activity / glucose-1-phosphatase activity / carbohydrate phosphatase activity / sugar-phosphatase activity / alkaline phosphatase / alkaline phosphatase activity / phosphate-containing compound metabolic process / periplasmic space / zinc ion binding / metal ion binding
Similarity search - Function
Gyrase A; domain 2 - #150 / Alkaline phosphatase, prokaryotic / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkaline phosphatase PafA
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.031 Å
AuthorsLyubimov, A.Y. / Sunden, F. / AlSadhan, I. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM64798 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution.
Authors: Sunden, F. / AlSadhan, I. / Lyubimov, A. / Doukov, T. / Swan, J. / Herschlag, D.
History
DepositionOct 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Alkaline phosphatase PafA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4176
Polymers61,1201
Non-polymers2975
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.329, 113.329, 69.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Alkaline phosphatase PafA / AP PafA


Mass: 61120.406 Da / Num. of mol.: 1 / Fragment: UNP residues 21-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: pafA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJX5, alkaline phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 32.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 22% PEG3350, 0.1 M sodium acetate, pH 4.4, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016
RadiationMonochromator: Si(111) Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.03→41.01 Å / Num. obs: 28568 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.6
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.518 / CC1/2: 0.66 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.96 Å41.01 Å
Translation6.96 Å41.01 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
Aimless0.5.27data scaling
PHASER2.6.0phasing
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TJ3

5tj3


Resolution: 2.031→41.009 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.01
RfactorNum. reflection% reflection
Rfree0.2086 1493 5.23 %
Rwork0.1704 --
obs0.1724 28561 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.1 Å2 / Biso mean: 40.6973 Å2 / Biso min: 16.98 Å2
Refinement stepCycle: final / Resolution: 2.031→41.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 5 217 4241
Biso mean--48.25 37.66 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134120
X-RAY DIFFRACTIONf_angle_d1.1845611
X-RAY DIFFRACTIONf_chiral_restr0.069622
X-RAY DIFFRACTIONf_plane_restr0.009721
X-RAY DIFFRACTIONf_dihedral_angle_d19.6381457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0312-2.09670.32251020.254624592561
2.0967-2.17170.26491800.236924062586
2.1717-2.25860.29341210.222224672588
2.2586-2.36140.27931490.210824492598
2.3614-2.48590.2241500.198724082558
2.4859-2.64160.22461470.181224482595
2.6416-2.84550.24161200.179524702590
2.8455-3.13180.24611290.177124762605
3.1318-3.58470.2061260.162124712597
3.5847-4.51540.1761280.136724882616
4.5154-41.01760.15021410.145825262667

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