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- PDB-1khj: E. COLI ALKALINE PHOSPHATASE MUTANT (D153HD330N) MIMIC OF THE TRA... -

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Basic information

Entry
Database: PDB / ID: 1khj
TitleE. COLI ALKALINE PHOSPHATASE MUTANT (D153HD330N) MIMIC OF THE TRANSITION STATES WITH ALUMINIUM FLUORIDE
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 homologues / Alkaline phosphatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsLe Du, M.H. / Lamoure, C. / Muller, B.H. / Bulgakov, O.V. / Lajeunesse, E. / Menez, A. / Boulain, J.C.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Artificial evolution of an enzyme active site: structural studies of three highly active mutants of Escherichia coli alkaline phosphatase.
Authors: Le Du, M.H. / Lamoure, C. / Muller, B.H. / Bulgakov, O.V. / Lajeunesse, E. / Menez, A. / Boulain, J.C.
#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
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 25, 2014Group: Database references
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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

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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)94,6618
Polymers94,2312
Non-polymers4306
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-132 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)163.511, 163.511, 138.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.00713, 0.999974, -0.001354), (0.999974, -0.007132, -0.001395), (-0.001404, -0.001344, -0.999998)
Vector: -0.1119, 0.262, 104.4689)

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Components

#1: Protein Alkaline phosphatase /


Mass: 47115.484 Da / Num. of mol.: 2 / Mutation: D153H, D330N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: WCC118 / Plasmid: PLIP4.0D153HD330N / 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-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, magnesium chloride, zinc sulfate, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.4 Mammonium sulfate1reservoir
210 mM1reservoirMgCl2
31 mM1reservoirZnSO4
4100 mMTris-HCl1reservoirpH8.0
530-40 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.54181
ReflectionResolution: 2.3→20 Å / Num. all: 49163 / Num. obs: 49163 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Rsym value: 0.011
Reflection shellResolution: 2.3→2.44 Å / Rsym value: 0.48 / % possible all: 95
Reflection
*PLUS
Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1KH4
Resolution: 2.3→10 Å / Cross valid method: IMPLOR-CYCLING TEST SETS / σ(F): 0 / Stereochemistry target values: XPLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2400 5 %RANDOM
Rwork0.18 ---
all0.18 49163 --
obs0.18 49163 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 12 439 6967
LS refinement shellResolution: 2.3→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 2400 5 %
Rwork0.257 --
obs--95 %
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_angle_deg1.617
X-RAY DIFFRACTIONx_dihedral_angle_deg24.288
X-RAY DIFFRACTIONx_improper_angle_deg1.44
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.257 / Rfactor obs: 0.257

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