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- PDB-1n9k: Crystal structure of the bromide adduct of AphA class B acid phos... -

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Basic information

Entry
Database: PDB / ID: 1n9k
TitleCrystal structure of the bromide adduct of AphA class B acid phosphatase/phosphotransferase from E. coli at 2.2 A resolution
ComponentsClass B acid phosphatase
KeywordsHYDROLASE / Class B acid phosphatase / DDDD acid phosphatase / metallo-enzyme bromide MAD
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
BROMIDE ION / Class B acid phosphatase / Class B acid phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 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 25, 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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)48,35819
Polymers47,1112
Non-polymers1,24717
Water6,846380
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)96,71638
Polymers94,2214
Non-polymers2,49434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area16140 Å2
ΔGint-111 kcal/mol
Surface area33400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.499, 92.616, 138.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1406-

HOH

21B-1379-

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.: 2
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-MG / MAGNESIUM ION


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


Mass: 79.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
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 M solution of NaBr
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: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.91957, 0.9204, 0.88561
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 8, 2002 / Details: Torodial mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.919571
20.92041
30.885611
ReflectionResolution: 2.2→20 Å / Num. all: 32466 / Num. obs: 32466 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.17 % / Biso Wilson estimate: 24.13 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1272 / % possible all: 96.6
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 32501 / % possible obs: 98.5 % / Redundancy: 7.3 % / Num. measured all: 256647
Reflection shell
*PLUS
% possible obs: 96.6 % / Redundancy: 7 % / Num. unique obs: 1272 / Num. measured obs: 10044 / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.24refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.32 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.359 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.203 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23111 1648 5.1 %RANDOM
Rwork0.18855 ---
all0.19069 30818 --
obs0.19069 30818 98.3 %-
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: 26.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati sigma a obs: 0.092 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 17 380 3683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0213372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9294584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1310.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022640
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3060.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1861.52088
X-RAY DIFFRACTIONr_mcangle_it2.03123384
X-RAY DIFFRACTIONr_scbond_it3.39231284
X-RAY DIFFRACTIONr_scangle_it5.2644.51200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 121 -
Rwork0.198 2255 -
obs-1151 96.6 %
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg6.2
X-RAY DIFFRACTIONr_chiral_restr0.1

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