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- PDB-1ani: ALKALINE PHOSPHATASE (D153H, K328H) -

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Basic information

Entry
Database: PDB / ID: 1ani
TitleALKALINE PHOSPHATASE (D153H, K328H)
ComponentsALKALINE PHOSPHATASE
KeywordsALKALINE PHOSPHATASE / HYDROLASE (PHOSPHORIC MONOESTER) / TRANSFERASE (PHOSPHO / ALCOHOL ACCEPTOR)
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 / 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 / Resolution: 2.5 Å
AuthorsMurphy, J.E. / Tibbitts, T.T. / Kantrowitz, E.R.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Mutations at positions 153 and 328 in Escherichia coli alkaline phosphatase provide insight towards the structure and function of mammalian and yeast alkaline phosphatases.
Authors: Murphy, J.E. / Tibbitts, T.T. / Kantrowitz, E.R.
#1: Journal: Biochemistry / Year: 1993
Title: Magnesium in the Active Site of Escherichia Coli Alkaline Phosphatase is Important for Both Structural Stabilization and Catalysis
Authors: Janeway, C.M.L. / Xu, X. / Murphy, J.E. / Chaidaroglou, A. / Kantrowitz, E.R.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Conversion of a Magnesium Binding Site Into a Zinc Binding Site by a Single Amino Acid Substitution in Escherichia Coli Alkaline Phosphatase
Authors: Murphy, J.E. / Xu, X. / Kantrowitz, E.R.
#3: 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.
History
DepositionSep 6, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)94,46513
Polymers93,5982
Non-polymers86711
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-236 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.600, 167.300, 76.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ALKALINE PHOSPHATASE


Mass: 46799.086 Da / Num. of mol.: 2 / Mutation: D153H, K328H
Source method: isolated from a genetically manipulated source
Details: 65% SATURATING (NH4)2SO4, 100 MM TRIS, 10 MM MGCL2, 10 MM ZNCL2, 2 MM NAH2PO4 AT PH 7.5
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EK1481 / Gene: PHOA / Plasmid: PEK190 / Gene (production host): PHOA / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / References: UniProt: P00634, alkaline phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlenzyme1drop
220 %satammonium sulfate1drop
3100 mMTris-HCl1drop
410 mM1dropMgCl2
50.01 mM1dropZnCl2
636-39 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SAN DIEGO MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 28, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→8 Å / Num. obs: 39775 / % possible obs: 91 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Num. measured all: 118201 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
SANDIEGO MULTIWIREdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
IMPLORrefinement
POLYVISIONrefinement
TIBBITTSrefinement
SDMSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.176 --
obs0.176 38348 91 %
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 31 270 6869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.98
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor Rfree: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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