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- PDB-3dpc: Structure of E.coli Alkaline Phosphatase Mutant in Complex with a... -

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Basic information

Entry
Database: PDB / ID: 3dpc
TitleStructure of E.coli Alkaline Phosphatase Mutant in Complex with a Phosphorylated Peptide
Components
  • Alkaline phosphatase
  • Phosphorylated Peptide
KeywordsHYDROLASE / alkaline phosphatase / complex structure / protein kinase / Magnesium / Metal-binding / Phosphoprotein
Function / homology
Function and homology information


oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / dephosphorylation / protein dephosphorylation / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, W.H. / Jiang, T.
CitationJournal: Biosens.Bioelectron. / Year: 2009
Title: Development of a universal phosphorylated peptide-binding protein for simultaneous assay of kinases
Authors: Li, W. / Bi, L. / Wang, W. / Li, Y. / Zhou, Y. / Wei, H. / Jiang, T. / Bai, L. / Chen, Y. / Zhang, Z. / Yuan, X. / Xiao, J. / Zhang, X.-E.
History
DepositionJul 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 5, 2014Group: Derived calculations
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: 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
C: Phosphorylated Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2925
Polymers97,0753
Non-polymers2172
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-38 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.862, 107.740, 148.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alkaline phosphatase / / APase


Mass: 47949.344 Da / Num. of mol.: 2 / Mutation: S102L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: phoA, b0383, JW0374 / Plasmid: pASK75 / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / References: UniProt: P00634, alkaline phosphatase
#2: Protein/peptide Phosphorylated Peptide


Mass: 1176.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence is chemically synthesized
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 314 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 39%-43% saturation ammonium sulfate, 100mM Tris pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 314K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 47078 / Num. obs: 46934 / % possible obs: 99.7 % / Redundancy: 7.51 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4641 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B8J

1b8j


Resolution: 2.3→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 3
RfactorNum. reflectionSelection details
Rfree0.2714 4693 Random
Rwork0.2336 --
all-46752 -
obs-42059 -
Displacement parametersBiso mean: 32.88 Å2
Baniso -1Baniso -2Baniso -3
1--4.217 Å20 Å20 Å2
2--10.09 Å20 Å2
3----5.873 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6687 0 13 221 6921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.598

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