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- PDB-1alk: REACTION MECHANISM OF ALKALINE PHOSPHATASE BASED ON CRYSTAL STRUC... -

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Basic information

Entry
Database: PDB / ID: 1alk
TitleREACTION MECHANISM OF ALKALINE PHOSPHATASE BASED ON CRYSTAL STRUCTURES. TWO METAL ION CATALYSIS
ComponentsALKALINE PHOSPHATASE
KeywordsALKALINE PHOSPHATASE
Function / homologyAlkaline phosphatase / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase, active site / Alkaline-phosphatase-like, core domain superfamily / Alkaline phosphatase-like, alpha/beta/alpha / oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity ...Alkaline phosphatase / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase, active site / Alkaline-phosphatase-like, core domain superfamily / Alkaline phosphatase-like, alpha/beta/alpha / 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 / Alkaline phosphatase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / 2 Å resolution
AuthorsKim, E.E. / Wyckoff, W.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis.
Authors: Kim, E.E. / Wyckoff, H.W.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Bacillus Subtilis Alkaline Phosphatases III and Iv. Cloning, Sequencing, and Comparisons of Deduced Amino Acid Sequence with Escherichia Coli Alkaline Phosphatase Three-Dimensional Structure
Authors: Hulett, F.M. / Kim, E.E. / Bookstein, C. / Kapp, N.V. / Edwards, C.W. / Wyckoff, H.W.
#2: Journal: Clin.Chim.Acta / Year: 1989
Title: Structure of Alkaline Phosphatases
Authors: Kim, E.E. / Wyckoff, H.W.
#3: Journal: J.Mol.Biol. / Year: 1985
Title: Refined Structure of Alkaline Phosphatase
Authors: Sowadski, J.M. / Handschumacher, M.D. / Murthy, H.M.K. / Foster, B.A. / Wyckoff, H.W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 3, 1993 / Release: Jan 31, 1994
RevisionDateData content typeGroupProviderType
1.0Jan 31, 1994Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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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)94,68710
Polyers94,1872
Non-polymers5008
Water1086
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8720
ΔGint (kcal/M)-205
Surface area (Å2)27920
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)195.300, 167.400, 76.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI 2 2 2
Atom site foot note1: RESIDUES 1-4 AND 404-409 ARE NOT WELL DEFINED IN THE ELECTRON DENSITY MAPS.
DetailsTHERE IS A DIMER (IDENTICAL CHAIN OF 449 RESIDUES) PER ASYMMETRIC UNIT AND THEY ARE REFINED INDEPENDENTLY.

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Components

#1: Protein/peptide ALKALINE PHOSPHATASE /


Mass: 47093.410 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Formula: PO4 / Phosphate
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Formula: H2O / Water
Nonpolymer detailsTHERE ARE THREE WATER MOLECULES COORDINATING TO THE THIRD METAL, NAMELY MG (RESIDUE NUMBER 452 ), ...THERE ARE THREE WATER MOLECULES COORDINATING TO THE THIRD METAL, NAMELY MG (RESIDUE NUMBER 452 ), AND THESE ARE NUMBERED 454 - 456.
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PPB_ECOLI SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 37 ASN 15 ASP 57 ASN 35 LYS 198 GLN 176 LYS 250 GLU 228 LYS 252 GLU 230

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 / Density percent sol: 63.02 %
Crystal grow
*PLUS
pH: 9.5 / Method: microdialysis
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
10.1 MTris-HCl11
20.01 M11MgCl2
35x10-5 M11Zn

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2 Å / Number obs: 17164 / Rmerge I obs: 0.047

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
Least-squares processR factor R work: 0.177 / R factor obs: 0.177 / Highest resolution: 2 Å
Refine hist #LASTHighest resolution: 2 Å
Number of atoms included #LASTProtein: 6608 / Nucleic acid: 0 / Ligand: 16 / Solvent: 6 / Total: 6630
Least-squares process
*PLUS
R factor obs: 0.177 / Highest resolution: 2 Å / Lowest resolution: 5 Å
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.96

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