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- PDB-1elz: E. COLI ALKALINE PHOSPHATASE MUTANT (S102G) -

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Basic information

Entry
Database: PDB / ID: 1elz
TitleE. COLI ALKALINE PHOSPHATASE MUTANT (S102G)
ComponentsALKALINE PHOSPHATASE
KeywordsHYDROLASE / ALKALINE PHOSPHATASE
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: 2.8 Å
AuthorsStec, B. / Hehir, M. / Brennan, C. / Nolte, M. / Kantrowitz, E.R.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Kinetic and X-ray structural studies of three mutant E. coli alkaline phosphatases: insights into the catalytic mechanism without the nucleophile Ser102.
Authors: Stec, B. / Hehir, M.J. / Brennan, C. / Nolte, 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
DepositionFeb 10, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Nov 3, 2021Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 9, 2023Group: Advisory / Derived calculations / Refinement description
Category: pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALKALINE PHOSPHATASE
B: ALKALINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,62910
Polymers94,1292
Non-polymers5008
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-220 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.570, 164.500, 138.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-487-

HOH

21A-583-

HOH

31A-658-

HOH

41A-720-

HOH

51B-483-

HOH

61B-523-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.005904, 0.999966, -0.005775), (0.999964, -0.005939, -0.006044), (-0.006078, -0.005739, -0.999965)
Vector: 0.1481, 0.4533, 104.515)

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Components

#1: Protein ALKALINE PHOSPHATASE /


Mass: 47064.375 Da / Num. of mol.: 2 / Mutation: S102G
Source method: isolated from a genetically manipulated source
Details: ENZYME INHIBITED WITH PHOSPHATE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SM547 / Gene: PHOA / Plasmid: PEK307 / 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 / 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 3.3 Å3/Da / Density % sol: 57.22 %
Crystal growpH: 7.5
Details: 25 MG/ML PROTEIN IN 39% SATURATING (NH4)2SO4, 100 MM TRIS, 10 MM MGCL2 100 MM ZNCL2, 2 MM NAH2PO4 AT PH 7.5, EQUILIBRATED AGAINST 55% SATURATING (NH4)2SO4
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
5100 mM1dropZnCl2
636-39 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jul 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→37 Å / Num. obs: 26363 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.4 / % possible all: 85
Reflection shell
*PLUS
% possible obs: 85 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ALK

1alk


Resolution: 2.8→9 Å / Isotropic thermal model: ALL ATOMS / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.173 4 10 %
Rwork0.138 --
obs0.138 22562 84 %
Displacement parametersBiso mean: 21.92 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 9 Å
Refinement stepCycle: LAST / Resolution: 2.8→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 16 677 7297
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.5
X-RAY DIFFRACTIONx_mcangle_it3.5
X-RAY DIFFRACTIONx_scbond_it3.5
X-RAY DIFFRACTIONx_scangle_it3.5
LS refinement shellResolution: 2.8→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2285 4 10 %
Rwork0.2051 761 -
obs--85 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor obs: 0.2051

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