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- PDB-2hf7: Transition State Analogue of AphA class B Acid Phosphatase/Phosph... -

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Basic information

Entry
Database: PDB / ID: 2hf7
TitleTransition State Analogue of AphA class B Acid Phosphatase/Phosphotransferase (Aluminium Fluoride Complex)
ComponentsClass B acid phosphatase
KeywordsHYDROLASE / Apha class B Acid phosphatase/phosphotransferase - Transition state analogue
Function / homology
Function and homology information


L-phosphoserine phosphatase activity / acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / magnesium ion binding / identical protein binding
Similarity search - Function
HAD-superfamily phosphatase, subfamily IIIB, AphA / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLeone, R. / Calderone, V. / Cappelletti, E. / Benvenuti, M. / Mangani, S.
Citation
#1: Journal: J.Mol.Biol. / Year: 2004
Title: The First Structure of a Bacterial Class B Acid Phosphatase Reveals Further Structural Heterogeneity Among Phosphatases of Haloacid Deahalogenase Fold
Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Thaller, M.C. / Rossolini, G.M. / Mangani, S.
#2: Journal: Biochim.Biophys.Acta / Year: 2006
Title: Biochemical Characterization of the Class B Acid Phosphatase (Apha) of Escherichia Coli Mg1655
Authors: Passariello, C. / Forleo, C. / Micheli, V. / Schippa, S. / Leone, R. / Mangani, S. / Thaller, M.C. / Rossolini, G.M.
#3: Journal: J.Mol.Biol. / Year: 2006
Title: A Structure-Based Proposal for the Catalytic Mechanism of Bacterial Acid Phosphatase Apha Belonging to the Dddd Superfamily of Phosphohydrolases
Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Thaller, M.C. / Rossolini, G.M. / Mangani, S.
History
DepositionJun 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 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 / pdbx_struct_special_symmetry / struct_conn / 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.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.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_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: Class B acid phosphatase
B: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1536
Polymers46,9372
Non-polymers2174
Water11,025612
1
A: Class B acid phosphatase
B: Class B acid phosphatase
hetero molecules

A: Class B acid phosphatase
B: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,30612
Polymers93,8734
Non-polymers4338
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13130 Å2
ΔGint-94 kcal/mol
Surface area33740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.430, 66.484, 91.624
Angle α, β, γ (deg.)90.00, 121.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-884-

HOH

21B-1071-

HOH

DetailsThe biological assembly is a homotetramer.

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Components

#1: Protein Class B acid phosphatase


Mass: 23468.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aphA, napA / Plasmid: pATAC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P0AE22, acid phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


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


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Reservoior: Na acetate 50mM, 18% (w/v) PEG6000, 0.6% (w/v) Spermine. Protein concentration: 4.16 mg/ml, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939239 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2006
RadiationMonochromator: Khozu monochromator with a McLennon controller containing a LN2 cooled Si111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939239 Å / Relative weight: 1
ReflectionResolution: 1.6→51.16 Å / Num. obs: 62575 / Redundancy: 7.2 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.448 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 2B82

2b82


Resolution: 1.6→51.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN BOTH CHAINS THE AL ATOM OF THE ALUMINIUM TRIFLUORIDE MOLECULE (AF3) IS LINKED BY A COORDINATION BOND TO ASP44 OD1 AND TO A WATER ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN BOTH CHAINS THE AL ATOM OF THE ALUMINIUM TRIFLUORIDE MOLECULE (AF3) IS LINKED BY A COORDINATION BOND TO ASP44 OD1 AND TO A WATER MOLECULE (A611 IN CHAIN A AND B612 IN CHAIN B). SINCE THERE IS NO DETECTABLE ELECTRON DENSITY HETEROGENEITY BETWEEN ALUMINIUM TRIFLUORIDE AND ALUMINIUM TETRAFLUORIDE, BOTH WATER MOLECULES, A611 AND A612, COULD BE FLUORINE ATOM.
RfactorNum. reflection% reflectionSelection details
Rfree0.19628 5734 9.2 %RANDOM
Rwork0.17123 ---
obs0.17351 56814 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.868 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20.43 Å2
2---0.42 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.6→51.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 10 612 3936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223408
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9434634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65524.146164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05315540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4841524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022672
X-RAY DIFFRACTIONr_nbd_refined0.1920.21699
X-RAY DIFFRACTIONr_nbtor_refined0.310.22384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2441
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.238
X-RAY DIFFRACTIONr_mcbond_it0.6971.52112
X-RAY DIFFRACTIONr_mcangle_it1.12523426
X-RAY DIFFRACTIONr_scbond_it1.81231296
X-RAY DIFFRACTIONr_scangle_it2.9144.51208
X-RAY DIFFRACTIONr_sphericity_free4.46632
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 445 -
Rwork0.225 4200 -
obs--100 %

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