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- PDB-3cz4: Native AphA class B acid phosphatase/phosphotransferase from E. coli -

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Basic information

Entry
Database: PDB / ID: 3cz4
TitleNative AphA class B acid phosphatase/phosphotransferase from E. coli
ComponentsClass B acid phosphatase
KeywordsHYDROLASE / ACID PHOSPHATASE/PHOSPHOTRANSFERASE / METALLO PHOSPHATASE / Magnesium / Metal-binding / Periplasm
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
ACETATE ION / Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLeone, R. / Cappelletti, E. / Benvenuti, M. / Lentini, G. / Thaller, M.C. / Mangani, S.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structural insights into the catalytic mechanism of the bacterial class B phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases.
Authors: Leone, R. / Cappelletti, E. / Benvenuti, M. / Lentini, G. / Thaller, M.C. / Mangani, S.
#1: 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.
History
DepositionApr 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,00910
Polymers23,5551
Non-polymers4539
Water5,837324
1
A: Class B acid phosphatase
hetero molecules

A: Class B acid phosphatase
hetero molecules

A: Class B acid phosphatase
hetero molecules

A: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,03540
Polymers94,2214
Non-polymers1,81436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area16390 Å2
ΔGint-144 kcal/mol
Surface area33500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.294, 92.775, 137.600
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-215-

CL

21A-216-

MG

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Class B acid phosphatase


Mass: 23555.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aphA, napA, yjbP, b4055, JW4015 / Plasmid: pATAC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(De3) / References: UniProt: P0AE22, acid phosphatase

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Non-polymers , 5 types, 333 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: drop: 4.2-3.5 mg/mL in 50 mM CH3COONa buffer at pH 7.2, 10 mM MgCl2 reservoir: 18% (w/v) polyethylene glycol (PEG) 6000, 0.6% (w/v) Spermine, 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: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2002
Details: Monochromator double crystal, Si(111); toroidal mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→8 Å / Num. obs: 31967 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 17.14 Å2 / Rsym value: 0.092 / Net I/σ(I): 4.4
Reflection shellResolution: 1.7→1.742 Å / Redundancy: 4.14 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2311 / Rsym value: 0.165 / % possible all: 99.51

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B82

2b82


Resolution: 1.7→7.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.728 / SU ML: 0.058 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21167 1717 5.1 %RANDOM
Rwork0.181 ---
all0.181 31967 --
obs0.181 31967 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 27 324 2031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221748
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9442375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.995222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.09824.02387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22415280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021378
X-RAY DIFFRACTIONr_nbd_refined0.1910.2832
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2248
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.230
X-RAY DIFFRACTIONr_mcbond_it0.6921.51089
X-RAY DIFFRACTIONr_mcangle_it1.17621735
X-RAY DIFFRACTIONr_scbond_it1.793743
X-RAY DIFFRACTIONr_scangle_it2.864.5633
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 116 -
Rwork0.251 2311 -
obs-2311 99.51 %

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