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- PDB-4d74: 1.57 A crystal structure of erwinia amylovora tyrosine phosphatas... -

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Basic information

Entry
Database: PDB / ID: 4d74
Title1.57 A crystal structure of erwinia amylovora tyrosine phosphatase amsI
ComponentsPROTEIN-TYROSINE-PHOSPHATASE AMSI
KeywordsHYDROLASE / AMYLOVORAN / TYROSINE PHOSPHATASE / PHOSPHATASE / AMSI / FIRE BLIGHT
Function / homology
Function and homology information


polysaccharide biosynthetic process / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity
Similarity search - Function
: / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable low molecular weight protein-tyrosine-phosphatase AmsI
Similarity search - Component
Biological speciesERWINIA AMYLOVORA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsBenini, S. / Salomone-Stagni, M. / Caputi, L. / Cianci, M.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Characterization and 1.57 A Resolution Structure of the Key Fire Blight Phosphatase Amsi from Erwinia Amylovora
Authors: Salomone-Stagni, M. / Musiani, F. / Benini, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Cloning, Purification, Crystallization and 1.57 A Resolution X-Ray Data Analysis of Amsi, the Tyrosine Phosphatase Controlling Amylovoran Biosynthesis in the Plant Pathogen Erwinia Amylovora.
Authors: Benini, S. / Caputi, L. / Cianci, M.
History
DepositionNov 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROTEIN-TYROSINE-PHOSPHATASE AMSI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2014
Polymers18,9131
Non-polymers2883
Water1,802100
1
A: PROTEIN-TYROSINE-PHOSPHATASE AMSI
hetero molecules

A: PROTEIN-TYROSINE-PHOSPHATASE AMSI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4028
Polymers37,8252
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area2430 Å2
ΔGint-93.1 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.026, 66.026, 72.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN-TYROSINE-PHOSPHATASE AMSI


Mass: 18912.697 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-144 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA AMYLOVORA (bacteria) / Strain: EA273 / Plasmid: PETM-11AMSI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46630, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.75 Å3/Da / Density % sol: 55.36 % / Description: NONE
Crystal growMethod: microbatch / pH: 5.5
Details: MICROBATCH UNDER OIL 1UL PROTEIN ADDED TO 1 UL AMMONIUM SULPHATE 1.7 M, 100MM SODIUM ACETATE PH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.57→72.27 Å / Num. obs: 25949 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19.7 % / Biso Wilson estimate: 16.85 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.2
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WMY

2wmy


Resolution: 1.57→57.18 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.186 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY RESIDUES NLYFQGA AT THE BEGINNING OF CHAIN A ARE PART OF THE N-TERMINAL HIS-TAG WHICH WAS NOT CLEAVED BEFORE CRYSTALLIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.17922 1318 5.1 %RANDOM
Rwork0.16881 ---
obs0.16934 24575 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.483 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.7 Å20 Å2
2--0.7 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.57→57.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 15 100 1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191200
X-RAY DIFFRACTIONr_bond_other_d0.0010.021172
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9641625
X-RAY DIFFRACTIONr_angle_other_deg0.80632691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.82224.61552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48915216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.434158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021357
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 97 -
Rwork0.208 1785 -
obs--99.63 %

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