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- PDB-1ed8: STRUCTURE OF E. COLI ALKALINE PHOSPHATASE INHIBITED BY THE INORGA... -

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Basic information

Entry
Database: PDB / ID: 1ed8
TitleSTRUCTURE OF E. COLI ALKALINE PHOSPHATASE INHIBITED BY THE INORGANIC PHOSPHATE AT 1.75A RESOLUTION
ComponentsALKALINE PHOSPHATASE
KeywordsHYDROLASE / wild type / inhibited by phosphate
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: 1.75 Å
AuthorsStec, B. / Holtz, K.M. / Kantrowitz, E.R.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: A revised mechanism for the alkaline phosphatase reaction involving three metal ions.
Authors: Stec, B. / Holtz, K.M. / Kantrowitz, E.R.
#1: 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
DepositionJan 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)95,01214
Polymers94,1892
Non-polymers82312
Water10,881604
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-293 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.150, 167.340, 76.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1514-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALKALINE PHOSPHATASE


Mass: 47094.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PEK48 / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase

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Non-polymers , 5 types, 616 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, ammonium sulfate, magnesium chloride, zinc chloride , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 9.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
220 %satammonium sulfate1drop
3100 mMTris-HCl1drop
410 mM1dropMgCl2
50.01 mM1dropZnCl2
639-43 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Aug 10, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→35 Å / Num. all: 116581 / Num. obs: 116581 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.0644 / Net I/σ(I): 10.8
Reflection shellResolution: 1.75→1.88 Å / Redundancy: 1.81 % / Rmerge(I) obs: 0.312 / Num. unique all: 18778 / % possible all: 75
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 74.5 % / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
SHELXL-97refinement
SDMSdata scaling
X-PLORphasing
RefinementResolution: 1.75→15 Å / Num. parameters: 30074 / Num. restraintsaints: 29173 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Conjugate gradient refinement. Last cycle with full matrix.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 4653 4 %every 25 reflection
Rwork0.196 ---
all0.197 116349 --
obs0.197 111696 92 %-
Solvent computationSolvent model: moews & kretsinger
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 6387 / Occupancy sum non hydrogen: 7235.9
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 28 604 7252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_from_restr_planes0.25
X-RAY DIFFRACTIONs_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.107
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4 % / Rfactor all: 0.196 / Rfactor obs: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d24.7
X-RAY DIFFRACTIONs_improper_angle_d1.82
X-RAY DIFFRACTIONs_plane_restr0.25
X-RAY DIFFRACTIONs_chiral_restr0.112

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