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- PDB-1ew9: ALKALINE PHOSPHATASE (E.C. 3.1.3.1) COMPLEX WITH MERCAPTOMETHYL P... -

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Basic information

Entry
Database: PDB / ID: 1ew9
TitleALKALINE PHOSPHATASE (E.C. 3.1.3.1) COMPLEX WITH MERCAPTOMETHYL PHOSPHONATE
ComponentsALKALINE PHOSPHATASE
KeywordsHYDROLASE / enzyme-inhibitor complex
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
MERCAPTOMETHYL PHOSPHONATE / Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHoltz, K.M. / Stec, B. / Meyers, J.K. / Antonelli, S.M. / Widlanski, T.S. / Kantrowitz, E.R.
Citation
Journal: Protein Sci. / Year: 2000
Title: Alternate modes of binding in two crystal structures of alkaline phosphatase-inhibitor complexes.
Authors: Holtz, K.M. / Stec, B. / Myers, J.K. / Antonelli, S.M. / Widlanski, T.S. / Kantrowitz, E.R.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: A Model of the Transition State in the Alkaline Phosphatase Reaction
Authors: Holtz, K.M. / Stec, B. / Kantrowitz, E.R.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Reaction Mechanism of Alkaline Phosphatase Based on Two Crystal Structures. Two-metal Ion Catalysis
Authors: Kim, E.E. / Wyckoff, H.W.
History
DepositionApr 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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)95,07414
Polymers94,1892
Non-polymers88512
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-291 kcal/mol
Surface area27590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)194.83, 167.10, 76.67
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1164-

HOH

Detailshomodimeric metalloenzyme with a non-crystallographic 2-fold symmetry axis

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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) / Strain: SM547 / Cellular location: PERIPLASM / Gene: PHOA / Plasmid: PEK154 / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase

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Non-polymers , 5 types, 569 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
Details: Myers, JK, Antonelli, SM, Widlanski, TS. 1997. Motifs for metallophosphatase inhibition. J. Am. Chem. Soc. 119: 3163-3164.
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MMQ / MERCAPTOMETHYL PHOSPHONATE


Mass: 126.071 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3O3PS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsThe magnesium 452 has three waters associated with it and it has been labelled as ligand MO3 for ...The magnesium 452 has three waters associated with it and it has been labelled as ligand MO3 for each chain. The zinc ion 452 has the same three waters associated with it and is labelled ZO3. The ZO3 and MO3 occupy the same space and have the same coordinates, but their occupancies are different. The MO3 is labelled as residue 452, conformation A. The ZO3 is labelled as residue 453, conformation B. SO4 558 is ASSOCIATED WITH CHAIN A, and SO4 958 is ASSOCIATED WITH CHAIN B.

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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: 3.31 Å3/Da / Density % sol: 62.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: enzyme: 30 mg/mL; buffer: 40% saturated ammonium sulfate, 100 mM Tris/10 mM magnesium sulfate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlenzyme1drop
220 %satammonium sulfate1reservoir
3100 mMTris1reservoir
410 mM1reservoirMgCl2
50.01 mM1reservoirZnCl2pH9.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Aug 26, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 84601 / Num. obs: 78354 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.15 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.257 / Num. unique all: 12128 / % possible all: 72.6
Reflection
*PLUS
Num. measured all: 202714
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 72.6 % / Mean I/σ(I) obs: 1.3

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
SHELXL-97refinement
SDMSdata scaling
X-PLORphasing
RefinementResolution: 2→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used conjugated gradient least squares for the refinement and weighted full matrix least squares procedure for estimating ESDs.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3115 -every 25
Rwork0.175 ---
all0.181 78354 --
obs0.181 77898 99.1 %-
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 30 557 7193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.028
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg24.8
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.89

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