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- PDB-1b8j: ALKALINE PHOSPHATASE COMPLEXED WITH VANADATE -

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Basic information

Entry
Database: PDB / ID: 1b8j
TitleALKALINE PHOSPHATASE COMPLEXED WITH VANADATE
ComponentsPROTEIN (ALKALINE PHOSPHATASE)
KeywordsALKALINE PHOSPHATASE / HYDROLASE / PHOSPHORIC MONOESTER / TRANSFERASE (PHOSPHO / ALCOHOL ACCEPTOR) / VANADATE
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
Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHoltz, K.M. / Stec, B. / Kantrowitz, E.R.
Citation
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.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Trapping and Visualization of a Covalent Enzyme-Phosphate Intermediate
Authors: Murphy, J.E. / Stec, B. / Ma, L. / Kantrowitz, E.R.
#2: 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 1, 1999Processing site: RCSB
Revision 1.0Feb 18, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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.ptnr2_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ALKALINE PHOSPHATASE)
B: PROTEIN (ALKALINE PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,92110
Polymers94,4192
Non-polymers5028
Water17,024945
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-105 kcal/mol
Surface area28040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)195.410, 167.810, 76.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.908718, 0.117698, -0.400474), (0.111158, -0.856542, -0.503964), (-0.402338, -0.502477, 0.765272)
Vector: 131.64729, 64.2954, 48.2772)

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Components

#1: Protein PROTEIN (ALKALINE PHOSPHATASE)


Mass: 47209.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VANADATE COVALENTLY BOUND TO SERINE NUCLEOPHILE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: SM547 / Cellular location: PERIPLASM / Gene: PHOA / Plasmid: PEK154 / Cellular location (production host): PERIPLASM / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 62.96 %
Crystal growpH: 7.5
Details: CRYSTALLIZATION CONDITIONS: 65 % SATURATING (NH4)2SO4, 100 MM TRIS, 10 MM MGCL2, 1 MM ZNCL2, 0.1 MM NH4VO3, PH 7.5
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
50.01 mM1dropZnCl2
636-39 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→26.42 Å / Num. obs: 93722 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 26.46 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 0.92 / % possible all: 85.3
Reflection
*PLUS
Num. measured all: 266977
Reflection shell
*PLUS
% possible obs: 85.3 %

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Processing

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

1alk


Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3 10 %RANDOM
Rwork0.177 ---
obs-86796 98.4 %-
Displacement parametersBiso mean: 19.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.275 Å0.25 Å
Luzzati d res low-8 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 16 945 7579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2

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