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- PDB-1n8n: Crystal structure of the Au3+ complex of AphA class B acid phosph... -

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Basic information

Entry
Database: PDB / ID: 1n8n
TitleCrystal structure of the Au3+ complex of AphA class B acid phosphatase/phosphotransferase from E. coli at 1.69 A resolution
ComponentsClass B acid phosphatase
KeywordsHYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme
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
GOLD 3+ ION / Class B acid phosphatase / Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsCalderone, V. / Forleo, C. / Benvenuti, M. / Rossolini, G.M. / Thaller, M.C. / Mangani, S.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: The first structure of a bacterial class B Acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold.
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.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)23,7522
Polymers23,5551
Non-polymers1971
Water5,116284
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)95,0098
Polymers94,2214
Non-polymers7884
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 area12110 Å2
ΔGint-84 kcal/mol
Surface area33650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.279, 92.457, 138.182
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-557-

HOH

DetailsThe biological assembly is a tetramer

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Components

#1: Protein Class B acid phosphatase / APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE


Mass: 23555.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: APHA / Production host: Escherichia coli (E. coli)
References: UniProt: P32697, UniProt: P0AE22*PLUS, acid phosphatase
#2: Chemical ChemComp-AU3 / GOLD 3+ ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 63.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K. The crystals of the native enzyme (containing Mg2+ or Zn2+) have been soaked in 1 mM solution of AuCl3
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
217-22 %PEG60001reservoir
31 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0377, 1.0404, 0.9392
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2002 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.03771
21.04041
30.93921
ReflectionResolution: 1.69→46.13 Å / Num. all: 31884 / Num. obs: 31884 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.709 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 7
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.093 / Mean I/σ(I) obs: 7 / Num. unique all: 2976 / Rsym value: 0.093 / % possible all: 53
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 98.2 % / Redundancy: 4.3 % / Num. measured all: 135549 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 92 % / Redundancy: 2.9 % / Num. unique obs: 2579 / Num. measured obs: 7369 / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD-phased Bromine derivative at 2.2 A resolution

Resolution: 1.69→46.13 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20698 1673 5.1 %RANDOM
Rwork0.17759 ---
all0.17906 31884 --
obs0.17906 31884 88.8 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.91 Å2
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.69→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 1 284 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211686
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9292292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055208
X-RAY DIFFRACTIONr_chiral_restr0.1080.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021320
X-RAY DIFFRACTIONr_nbd_refined0.1970.2779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.229
X-RAY DIFFRACTIONr_mcbond_it0.8981.51044
X-RAY DIFFRACTIONr_mcangle_it1.63421692
X-RAY DIFFRACTIONr_scbond_it2.6953642
X-RAY DIFFRACTIONr_scangle_it4.6234.5600
LS refinement shellResolution: 1.69→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 148 -
Rwork0.284 292 -
obs-2976 53 %
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5.6
X-RAY DIFFRACTIONr_chiral_restr0.1

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