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- PDB-1ajd: THREE-DIMENSIONAL STRUCTURE OF THE D153G MUTANT OF E. COLI ALKALI... -

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Basic information

Entry
Database: PDB / ID: 1ajd
TitleTHREE-DIMENSIONAL STRUCTURE OF THE D153G MUTANT OF E. COLI ALKALINE PHOSPHATASE: A MUTANT WITH WEAKER MAGNESIUM BINDING AND INCREASED CATALYTIC ACTIVITY
ComponentsALKALINE PHOSPHATASE INTERMEDIATE II OF HOLO ENZYME
KeywordsNON SPECIFIC MONO-ESTERASE
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
Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsDealwis, C.G. / Chen, L. / Abad-Zapatero, C.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystallographic analysis of reversible metal binding observed in a mutant (Asp153-->Gly) of Escherichia coli alkaline phosphatase.
Authors: Dealwis, C.G. / Brennan, C. / Christianson, K. / Mandecki, W. / Abad-Zapatero, C.
#1: Journal: To be Published
Title: Crystallographic Analysis of Reversible Metal Binding Observed in a Mutant (Asp153-->Gly) of E.Coli Alkaline Phosphatase
Authors: Dealwis, C. / Brennan, C. / Christianson, K. / Mandecki, W. / Abad-Zapatero, A.
#2: Journal: Protein Eng. / Year: 1992
Title: 3-D Structure of the (Asp101-->Ser) of E.Coli Alkaline Phosphatase with Higher Catalytic Activity
Authors: Chen, L. / Neidhart, D. / Kohlbrenner, M. / Mandecki, W. / Bell, S. / Sowadski, J. / Abad-Zapatero, C.
History
DepositionAug 18, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 4, 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_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_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
Remark 700SHEET SHEET DETERMINATION METHOD: KABSCH & SANDER; SHEET_ID: S1A; SAME AS 1ALK. SHEET_ID: S2A; SAME ...SHEET SHEET DETERMINATION METHOD: KABSCH & SANDER; SHEET_ID: S1A; SAME AS 1ALK. SHEET_ID: S2A; SAME AS 1ALK. SHEET_ID: S1B; SAME AS 1ALK. SHEET_ID: S2B; SAME AS 1ALK. SHEET_ID: S1B; REMARK IDENTIFIER: S2A SAME AS 1ALK.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALKALINE PHOSPHATASE INTERMEDIATE II OF HOLO ENZYME
B: ALKALINE PHOSPHATASE INTERMEDIATE II OF HOLO ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3858
Polymers94,0752
Non-polymers3106
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-138 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.020, 166.930, 76.440
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 INTERMEDIATE II OF HOLO ENZYME


Mass: 47037.348 Da / Num. of mol.: 2 / Mutation: D153G
Source method: isolated from a genetically manipulated source
Details: MUTANT WITH 4-FOLD INCREASED ACTIVITY AND WEAKER MG BINDING, STRUCTURE SOLVED AFTER RESOAKING METAL IONS FOR TWO MONTHS INTO THE APO CRYSTALS
Source: (gene. exp.) Escherichia coli (E. coli) / Description: LAC PROMOTER / Gene: PHOA / Plasmid: PWM528 AS BAMH1/HINDIII RESTRICTION FRAGMENT / Gene (production host): PHOA / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.78 %
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
220 %ammonium sulfate1drop
3100 mMTris-HCl1drop
410 mM1dropMgSO4
50.01 mM1dropZnCl2
631.6 %ammonium sulfate1reservoir
7100 mMTris-HCl1reservoir
810 mM1reservoirMgSO4

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 6, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 40175 / % possible obs: 77 % / Observed criterion σ(I): 0 / Redundancy: 1.55 % / Rmerge(I) obs: 0.127
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 24115 / % possible obs: 74.3 % / Rmerge(I) obs: 0.127

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Processing

Software
NameClassification
R-AXISdata collection
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 2.5→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.162 -
obs0.162 34945
Displacement parametersBiso mean: 11 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 6 4 6610
Refine LS restraints
Refine-IDTypeDev ideal
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_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Highest resolution: 2.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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