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- PDB-1rmt: Crystal structure of AphA class B acid phosphatase/phosphotransfe... -

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Basic information

Entry
Database: PDB / ID: 1rmt
TitleCrystal structure of AphA class B acid phosphatase/phosphotransferase complexed with adenosine.
ComponentsClass B acid phosphatase
KeywordsHYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme / adenosine.
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 / metal ion 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 / Class B acid phosphatase / Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCalderone, V. / Forleo, C. / Benvenuti, M. / Rossolini, G.M. / Thaller, M.C. / Mangani, S.
Citation
Journal: To be Published
Title: Insights in the catalytic mechanism of AphA from Escherichia coli
Authors: Calderone, V. / Forleo, C. / Benvenuti, M. / Rossolini, G.M. / Thaller, M.C. / 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. / M Rossolini, G. / Mangani, S.
History
DepositionNov 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
C: Class B acid phosphatase
D: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,38812
Polymers94,2214
Non-polymers1,1668
Water22,2121233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Class B acid phosphatase
D: Class B acid phosphatase
hetero molecules

B: Class B acid phosphatase
C: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,38812
Polymers94,2214
Non-polymers1,1668
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area14350 Å2
ΔGint-90 kcal/mol
Surface area33120 Å2
MethodPISA
3
A: Class B acid phosphatase
D: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6946
Polymers47,1112
Non-polymers5834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: Class B acid phosphatase
C: Class B acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6946
Polymers47,1112
Non-polymers5834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.740, 66.704, 88.556
Angle α, β, γ (deg.)90.00, 117.13, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer and there is a tetramer in the asymmetric unit.

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Components

#1: Protein
Class B acid phosphatase


Mass: 23555.342 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: APHA, NAPA, B4055, SF4149, S3580 / Plasmid: pATac / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P32697, UniProt: P0AE22*PLUS, acid phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1233 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Crystallization components* AphA 6mg/mL, 50mM Na acetate, 25% PEG 6000, 10mM adenosine, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.96111 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2002
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96111 Å / Relative weight: 1
ReflectionResolution: 1.4→75.419 Å / Num. all: 153897 / Num. obs: 153897 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 3.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.452 / % possible all: 59.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N8N

1n8n


Resolution: 1.4→74.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.205 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19908 11010 7.2 %RANDOM
Rwork0.16669 ---
obs0.16906 142874 100 %-
all-142874 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.611 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.08 Å2
2---0.33 Å20 Å2
3---0.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.046 Å
Refinement stepCycle: LAST / Resolution: 1.4→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 80 1233 7903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216848
X-RAY DIFFRACTIONr_bond_other_d0.0060.026000
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9449318
X-RAY DIFFRACTIONr_angle_other_deg0.853314004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7915834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027698
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021418
X-RAY DIFFRACTIONr_nbd_refined0.220.21453
X-RAY DIFFRACTIONr_nbd_other0.2590.27065
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2780
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.2229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.276
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.141.54192
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6826792
X-RAY DIFFRACTIONr_scbond_it2.36832656
X-RAY DIFFRACTIONr_scangle_it3.5744.52526
X-RAY DIFFRACTIONr_rigid_bond_restr1.28526848
X-RAY DIFFRACTIONr_sphericity_free3.321237
X-RAY DIFFRACTIONr_sphericity_bonded2.38626666
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 490
Rwork0.285 6229

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