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- PDB-1urb: ALKALINE PHOSPHATASE (N51MG) -

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Basic information

Entry
Database: PDB / ID: 1urb
TitleALKALINE PHOSPHATASE (N51MG)
ComponentsALKALINE PHOSPHATASE
KeywordsALKALINE PHOSPHATASE / HYDROLASE / PHOSPHORIC MONOESTER / PHOSPHO TRANSFERASE / ALCOHOL ACCEPTOR
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: 2.14 Å
AuthorsTibbitts, T.T. / Murphy, J.E. / Kantrowitz, E.R.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Kinetic and structural consequences of replacing the aspartate bridge by asparagine in the catalytic metal triad of Escherichia coli alkaline phosphatase.
Authors: Tibbitts, T.T. / Murphy, J.E. / Kantrowitz, E.R.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Mutations at Positions 153 and 328 in Escherichia Coli Alkaline Phosphatase Provide Insight Towards the Structure and Function of Mammalian and Yeast Alkaline Phosphatases
Authors: Murphy, J.E. / Tibbitts, T.T. / Kantrowitz, E.R.
#2: Journal: Protein Sci. / Year: 1994
Title: Kinetics and Crystal Structure of a Mutant E. Coli Alkaline Phosphatase (Asp-369->Asn): A Mechanism Involving One Zinc Per Active Site
Authors: Tibbitts, T.T. / Xu, X. / Kantrowitz, E.R.
#3: 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 3, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_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 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)94,09110
Polymers93,5322
Non-polymers5598
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8700 Å2
ΔGint-137 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.720, 168.480, 76.330
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
11A-575-

HOH

21B-587-

HOH

DetailsTHERE IS A DIMER (IDENTICAL CHAINS OF 449 RESIDUES) PER ASYMMETRIC UNIT. THESE SUBUNITS ARE DESIGNATED "A" AND "B".

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Components

#1: Protein ALKALINE PHOSPHATASE


Mass: 46766.074 Da / Num. of mol.: 2 / Mutation: D51N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EK1734 / Gene: PHOA / Plasmid: PEK247 / Gene (production host): PHOA / Production host: Escherichia coli (E. coli) / Strain (production host): SM547 / References: UniProt: P00634, alkaline phosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE IS OF A MUTANT ALKALINE PHOSPHATE (D51N) IN WHICH ASP-51 IS REPLACED BY ASN. THERE ...THE STRUCTURE IS OF A MUTANT ALKALINE PHOSPHATE (D51N) IN WHICH ASP-51 IS REPLACED BY ASN. THERE ARE TWO ZINCS COMPLEXED WITH AN INORGANIC PHOSPHATE BOUND IN EACH OF THE TWO ACTIVE SITES. THE THIRD METAL BIN SITE IS UNOCCUPIED.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growpH: 9.2
Details: 45% SATURATING (NH4)2SO4, 0.10 MM CAPS, 20 MM MGCL2, 10 UM ZNCL2, 0.1 MM NAH2PO4 AT PH 9.2.
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, hanging drop / Details: Chen, L. C., (1992) Protein Eng., 5, 605.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(w/v)1drop(NH4)2SO4
2100 mMTris1drop
310 mM1dropMgSO4
40.01 mM1dropZnCl2
530 mg/mlprotain1drop
631.6 %(w/v)1reservoir(NH4)2SO4
7100 mMTris1reservoir
810 mM1reservoirMgSO4

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Data collection

DetectorDate: Sep 28, 1994
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 61905 / % possible obs: 88.3 % / Observed criterion σ(I): 3
Reflection
*PLUS
Highest resolution: 2.14 Å / Redundancy: 3 % / Num. measured all: 186425 / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.14→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.241 -
Rwork0.193 -
obs0.193 59934
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.14→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6562 0 24 439 7025
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_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55

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