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- PDB-2wjf: Crystal structure of the tyrosine phosphatase Cps4B from Steptoco... -

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Basic information

Entry
Database: PDB / ID: 2wjf
TitleCrystal structure of the tyrosine phosphatase Cps4B from Steptococcus pneumoniae TIGR4 in complex with phosphate.
ComponentsTYROSINE-PROTEIN PHOSPHATASE CPSB
KeywordsHYDROLASE / CAPSULE BIOGENESIS/DEGRADATION / MANGANESE / PHOSPHATASE / PROTEIN PHOSPHATASE / EXOPOLYSACCHARIDE SYNTHESIS
Function / homology
Function and homology information


capsule polysaccharide biosynthetic process / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / manganese ion binding
Similarity search - Function
: / Capsular polysaccharide synthesis, CpsB/CapC / Capsular polysaccharide synthesis, CpsB/CapC / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Tyrosine-protein phosphatase CpsB
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsHagelueken, G. / Huang, H. / Naismith, J.H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structures of Wzb of Escherichia Coli and Cpsb of Streptococcus Pneumoniae, Representatives of Two Families of Tyrosine Phosphatases that Regulate Capsule Assembly.
Authors: Hagelueken, G. / Huang, H. / Mainprize, I.L. / Whitfield, C. / Naismith, J.H.
History
DepositionMay 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: 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 / 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_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE CPSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7515
Polymers28,4911
Non-polymers2604
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.980, 58.700, 115.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE CPSB / CPS4B


Mass: 28490.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR 4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9AHD4, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.27 Å3/Da / Density % sol: 45.36 % / Description: NONE
Crystal growDetails: 0.1 M NA-ACETATE, 35% W/V PEG 400, PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 15250 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.4 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNRELEASED STRUCTURE

Resolution: 2.22→25.86 Å / SU ML: 0.67 / σ(F): 1.35 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 787 5.2 %
Rwork0.158 --
obs0.161 15207 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.61 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 2.22→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 8 290 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072095
X-RAY DIFFRACTIONf_angle_d0.9462837
X-RAY DIFFRACTIONf_dihedral_angle_d14.759822
X-RAY DIFFRACTIONf_chiral_restr0.062313
X-RAY DIFFRACTIONf_plane_restr0.004367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2218-2.36090.23291270.15192313X-RAY DIFFRACTION98
2.3609-2.54310.22621270.15422369X-RAY DIFFRACTION100
2.5431-2.79870.24381390.15392390X-RAY DIFFRACTION100
2.7987-3.20310.23551360.16552387X-RAY DIFFRACTION100
3.2031-4.0330.20441300.14712434X-RAY DIFFRACTION100
4.033-25.86520.20591280.15492527X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.9256 Å / Origin y: -9.3171 Å / Origin z: 17.4734 Å
111213212223313233
T0.0669 Å2-0.0052 Å2-0.0034 Å2-0.0773 Å2-0.0105 Å2--0.0673 Å2
L0.1832 °20.0268 °20.0724 °2-0.2675 °2-0.1118 °2--0.3007 °2
S0.0049 Å °-0.0344 Å °0.0243 Å °0.0086 Å °-0.0246 Å °0.0134 Å °0.0019 Å °-0.0432 Å °0.0169 Å °
Refinement TLS groupSelection details: CHAIN A

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