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- PDB-2b8j: Crystal structure of AphA class B acid phosphatase/phosphotransfe... -

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Basic information

Entry
Database: PDB / ID: 2b8j
TitleCrystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate at 2 A resolution
Componentsclass B acid phosphatase
KeywordsHYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme / AMP
Function / homology
Function and homology information


L-phosphoserine phosphatase activity / acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / magnesium ion binding / metal 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
ADENOSINE / : / GOLD 3+ ION / PHOSPHATE ION / SPERMINE / Class B acid phosphatase / Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.033 Å
AuthorsCalderone, V. / Forleo, C. / Benvenuti, M. / Thaller, M.C. / Rossolini, G.M. / Mangani, S.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: A structure-based proposal for the catalytic mechanism of the 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.
#1: Journal: FEMS Microbiol.Lett. / Year: 1997
Title: Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product
Authors: Thaller, M.C. / Schippa, S. / Bonci, A. / Cresti, S. / Rossolini, G.M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Expression, purification, crystallization and preliminary X-ray characterization of the class B acid phosphatase (AphA) from Escherichia coli
Authors: Forleo, C. / Benvenuti, M. / Calderone, V. / Schippa, S. / Docquier, J.D. / Thaller, M.C. / Rossolini, G.M. / Mangani, S.
History
DepositionOct 7, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionNov 29, 2005ID: 1RM7
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_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_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.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_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)47,9449
Polymers46,9372
Non-polymers1,0077
Water3,765209
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)95,88718
Polymers93,8734
Non-polymers2,01414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15960 Å2
ΔGint-127 kcal/mol
Surface area32820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.966, 66.544, 91.544
Angle α, β, γ (deg.)90.00, 124.02, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer, but there is a dimer in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein class B acid phosphatase / E.C.3.1.3.2 / AphA


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 / Production host: Escherichia coli (E. coli)
References: UniProt: P32697, UniProt: P0AE22*PLUS, acid phosphatase

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Non-polymers , 7 types, 216 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#6: Chemical ChemComp-AU3 / GOLD 3+ ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#7: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, 10mM AMP, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.001 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2003 / Details: Double-crystal monochromator
RadiationMonochromator: double-crystal monochromator plus Si(111) and Si(220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 2.033→49.65 Å / Num. all: 28127 / Num. obs: 28127 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 19.44 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 6.2
Reflection shellResolution: 2.033→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3767 / Rsym value: 0.147 / % possible all: 89.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8N

1n8n


Resolution: 2.033→49.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22258 2330 8.3 %RANDOM
Rwork0.17123 ---
all0.17545 25795 --
obs0.17545 25795 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: 18.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.84 Å2
2---0.75 Å20 Å2
3---0.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.111 Å
Refinement stepCycle: LAST / Resolution: 2.033→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 42 209 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223438
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9524674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1625420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.10824.146164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27315539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8571524
X-RAY DIFFRACTIONr_chiral_restr0.1080.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21602
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22348
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.290
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8691.52112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5623426
X-RAY DIFFRACTIONr_scbond_it2.57831326
X-RAY DIFFRACTIONr_scangle_it4.1174.51248
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.033→2.086 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 140 -
Rwork0.19 1610 -
obs--100 %

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