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- PDB-2heg: Phospho-Aspartyl Intermediate Analogue of Apha class B acid phosp... -

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Basic information

Entry
Database: PDB / ID: 2heg
TitlePhospho-Aspartyl Intermediate Analogue of Apha class B acid phosphatase/phosphotransferase
ComponentsClass B acid phosphatase
KeywordsHYDROLASE / Apha class B Acid Phosphatase/Phosphotransferase
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
Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 21, 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 / 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 / _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

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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)47,1154
Polymers47,0672
Non-polymers492
Water16,069892
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)94,2308
Polymers94,1334
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12030 Å2
ΔGint-101 kcal/mol
Surface area33750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.428, 66.631, 90.103
Angle α, β, γ (deg.)90.00, 119.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

21A-597-

HOH

31A-641-

HOH

41A-644-

HOH

51B-530-

HOH

61B-567-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations:x,y,z, 1-x,y,1-z

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Components

#1: Protein Class B acid phosphatase


Mass: 23533.264 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: reservoir: Na acetate 50mM, PEG6000 18% (w/v), 0.6% Spermine (w/v) protein concentration: 3.5 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: 1.5→51.23 Å / Num. obs: 75720 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.358 / % possible all: 100

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Processing

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

2b82


Resolution: 1.5→51.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18943 6952 9.2 %RANDOM
Rwork0.16408 ---
obs0.16643 68744 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: 14.772 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.39 Å2
2---0.18 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 2 892 4216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223406
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9484630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9335416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01524.074162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34815538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691524
X-RAY DIFFRACTIONr_chiral_restr0.080.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022656
X-RAY DIFFRACTIONr_nbd_refined0.2360.21736
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2653
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.273
X-RAY DIFFRACTIONr_mcbond_it0.5191.52108
X-RAY DIFFRACTIONr_mcangle_it0.96723414
X-RAY DIFFRACTIONr_scbond_it1.58231298
X-RAY DIFFRACTIONr_scangle_it2.624.51216
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 482 -
Rwork0.22 5077 -
obs--100 %

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